MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Algorithms for Molecular Biology' source. Thu, 09 Feb 2012 16:56:35 +0100 http://www.medworm.com/index.php?rid=5635383&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F7%2F1%2F3 Conclusions: SuperFine+MRP when based upon a good MRP heuristic such as TNT, produces among the best scores for both MRP and MRL, and is generally faster and more topologically accurate than other supertree methods we tested. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5635383 Thu, 26 Jan 2012 05:00:00 +0100 5635383 http://www.medworm.com/index.php?rid=5603988&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F7%2F1%2F2 Conclusions: The proposed method can handle several control samples allowing for correction of multiple sources of bias simultaneously. Our evaluation on both synthetic and experimental data suggests that the method is successful in removing background noise. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5603988 Mon, 16 Jan 2012 05:00:00 +0100 5603988 http://www.medworm.com/index.php?rid=5592973&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F7%2F1%2F1 Conclusion: We have developed a method of identifying pathways associated with a quantitative trait using information on QTL. Our approach provides insights into genotype-phenotype relations at the level of biological pathways which may help to elucidate the genetic architecture underlying variation in phenotypic traits. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5592973 Sun, 15 Jan 2012 05:00:00 +0100 5592973 http://www.medworm.com/index.php?rid=5473650&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F27 Conclusions: A regularized elimination algorithm based on Partial Least Squares produces results that increase understandability and consistency and reduces the classification error on test data compared to standard approaches. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5473650 Mon, 05 Dec 2011 05:00:00 +0100 5473650 http://www.medworm.com/index.php?rid=5447626&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F26 Conclusions: The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from www.tbi.univie.ac.at/RNA (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5447626 Thu, 24 Nov 2011 05:00:00 +0100 5447626 http://www.medworm.com/index.php?rid=5355361&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F25 Conclusion: We revealed criteria allowing to specify conditions of preferred applicability for the local and the global alignment algorithms depending on positions and relative lengths of the cores and nonhomologous parts of the sequences to be aligned. It was demonstrated that when the core part of one sequence was positioned above the core of the other sequence, the global algorithm was more stable at longer evolutionary distances and larger nonhomologous parts than the local algorithm. On the contrary, when the cores were positioned asymmetrically, the local algorithm was more stable at longer evolutionary distances and larger nonhomologous parts than the global algorithm. This opens a possibility for creation of a combined method allowing generation of more accurate alignments. (Source... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5355361 Thu, 27 Oct 2011 04:00:00 +0100 5355361 http://www.medworm.com/index.php?rid=5310740&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F24 Conclusion: A number of experimental results shows that our random generation method produces realistic output, at least with respect to the appearance of the different structural motifs.The algorithm is available as a webservice at http://wwwagak.cs.uni-kl.de/NonUniRandGen and can be used for generating random secondary structures of any specified RNA type. A link to download an implementation of our method (in Wolfram Mathematica) can be found there, too. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5310740 Wed, 12 Oct 2011 04:00:00 +0100 5310740 http://www.medworm.com/index.php?rid=5310741&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F23 The growing volume of generated DNA sequencing data makes the problem of its long term storage increasingly important. In this work we present ReCoil -- an I/O efficient external memory algorithm designed for compression of very large collections of short reads DNA data. Typically each position of DNA sequence is covered by multiple reads of a short read dataset and our algorithm makes use of resulting redundancy to achieve high compression rate.While compression based on encoding mismatches between the dataset and a similar reference can yield high compression rate, good quality reference sequence may be unavailable. Instead, ReCoil's compression is based on encoding the differences between similar or overlapping reads. As such reads may appear at large distances from each other in the da... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5310741 Tue, 11 Oct 2011 04:00:00 +0100 5310741 http://www.medworm.com/index.php?rid=5246292&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F22 Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5246292 Thu, 22 Sep 2011 04:00:00 +0100 5246292 http://www.medworm.com/index.php?rid=5375270&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F21 Conclusions: Several biologically relevant special cases of the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5375270 Thu, 25 Aug 2011 04:00:00 +0100 5375270 http://www.medworm.com/index.php?rid=5168839&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F21 Conclusions: Several biologically relevant special cases of theNP-hard problem can be solved to optimality. In this way,parameterized analysis yields both deeper insight into thecomputational complexity and practical solving strategies. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5168839 Wed, 24 Aug 2011 23:00:00 +0100 5168839 http://www.medworm.com/index.php?rid=5155601&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F20 Conclusions: The algorithms presented in this paper improve the theoretical asymptotic worst case running time bounds for a large family of important problems. It is also possible that the suggested techniques could be applied to yield a practical speedup for these problems. For some of the problems (such as computing the RNA partition function and base-pair binding probabilities), the presented techniques are the only ones which are currently known for reducing the asymptotic running time bounds of the standard algorithms. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=5155601 Wed, 17 Aug 2011 23:00:00 +0100 5155601 http://www.medworm.com/index.php?rid=4974656&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F19 Conclusions: We compared our PromoBot algorithm to five other algorithms. It was found that the sensitivity and specificity of PromoBot performed as well as (or better than) the algorithms tested. These results show that the two proposed feature selection methods based on hexamer frequencies and random triplet-pair could be successfully incorporated into a supervised machine learning method. As such, we expect that PromoBot can be used to help identify new plant promoters. Source codes and analysis results of this work will be provided upon request. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4974656 Mon, 27 Jun 2011 23:00:00 +0100 4974656 http://www.medworm.com/index.php?rid=4967576&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F18 Conclusions: We demonstrate that the DeBi algorithm provides functionally more coherent gene sets compared to standard clustering or biclustering algorithms using biological validation measures such as Gene Ontology term and Transcription Factor Binding Site enrichment. We show that DeBi is a computationally efficient and powerful tool in analyzing large data sets. The method is also applicable on multiple gene expression data sets coming from different labs or platforms. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4967576 Wed, 22 Jun 2011 23:00:00 +0100 4967576 http://www.medworm.com/index.php?rid=4932212&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F17 Conclusions: MMMvII will thus allow for more more extensive and intricate analyses of coevolution.AvailabilityAn implementation of the MMMvII algorithm is available at: http://www.uhnresearch.ca/labs/tillier/MMMWEBvII/MMMWEBvII.php (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4932212 Mon, 13 Jun 2011 23:00:00 +0100 4932212 http://www.medworm.com/index.php?rid=4910370&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F16 Conclusions: Our algorithm satisfies the requirements of an automated methodology that combines highaccuracy with efficiency in analyzing SMFS datasets. The algorithm tackles the force spectroscopy analysisbottleneck leading to more consistent and reproducible results.Keywordsprotein unfolding, single-molecule force spectroscopy, pattern recognition, Force-Distance curve. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4910370 Sun, 05 Jun 2011 23:00:00 +0100 4910370 http://www.medworm.com/index.php?rid=4901247&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F15 Conclusions: We have implemented our algorithmand two of the best competitors. Our new algorithm issignificantly faster than the competition and seems to runin close to quadratic time in practice. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4901247 Thu, 02 Jun 2011 23:00:00 +0100 4901247 http://www.medworm.com/index.php?rid=4882723&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F14 Conclusions: The results demonstrate that our WDCM produces clusters with more consistent functional annotations than the other methods. The WDCM is also verified to be robust and is capable of clustering gene expression data containing a small quantity of missing values. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4882723 Mon, 30 May 2011 23:00:00 +0100 4882723 http://www.medworm.com/index.php?rid=4741759&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F13 Conclusions: The conclusions of this work are twofold. First, post-processing the output of combinatorial algorithms by incorporating prior information leads to a very efficient and effective motif discovery method. Second, combining priors from different sources is even more beneficial than considering them separately. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4741759 Thu, 21 Apr 2011 23:00:00 +0100 4741759 http://www.medworm.com/index.php?rid=4732576&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F7 Conclusions: Our results show that supertree methods that improve upon MRP are possible, and that an effort should be made to produce scalable and robust implementations of the most accurate supertree methods. Also, because topological accuracy depends upon taxon sampling strategies, attempts to construct very large phylogenetic trees using supertree methods should consider the selection of source tree datasets, as well as supertree methods. Finally, since supertree topological error is only weakly correlated with the supertree's topological distance to its source trees, development and testing of supertree methods presents methodological challenges. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4732576 Mon, 18 Apr 2011 23:00:00 +0100 4732576 http://www.medworm.com/index.php?rid=4732575&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F8 Conclusions: This algorithm infers haplotypes for a small number of sites, which can be useful for genetic disease studies to track down how changes in haplotypes such as recombinations relate to genetic disease. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4732575 Mon, 18 Apr 2011 23:00:00 +0100 4732575 http://www.medworm.com/index.php?rid=4732574&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F9 Conclusions: Empirical experiments on both synthetic and real RNA-Seq datasets show that IsoEM has scalable running time and outperforms existing methods of isoform and gene expression level estimation. Simulation experiments confirm previous findings that, for a fixed sequencing cost, using reads longer than 25-36 bases does not necessarily lead to better accuracy for estimating expression levels of annotated isoforms and genes. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4732574 Mon, 18 Apr 2011 23:00:00 +0100 4732574 http://www.medworm.com/index.php?rid=4732573&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F10 Conclusions: Two algorithms are introduced: an exponential-time hidden Markov model (HMM) for haplotype data where some individuals are untyped, and a linear-time algorithm for pedigrees having haplotype data for all individuals. Recombination estimates from the general haplotype HMM algorithm are compared to recombination estimates produced by a genotype HMM. Having haplotype data on all individuals produces better estimates. However, having several untyped individuals can drastically reduce the utility of haplotype data. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4732573 Mon, 18 Apr 2011 23:00:00 +0100 4732573 http://www.medworm.com/index.php?rid=4732572&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F11 We describe an average-case O(n^2) algorithm to list all reversals on a signed permutation pi that, when applied to pi, produce a permutation that is closer to the identity. This algorithm is optimal in the sense that, the time it takes to write the list is Omega(n^2) in the worst case. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4732572 Mon, 18 Apr 2011 23:00:00 +0100 4732572 http://www.medworm.com/index.php?rid=4732571&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F12 Background: Proteins are dynamic molecules that exhibit a wide range of motions; often these conformational changes are important for protein function. Determining biologically relevant conformational changes, or true variability, efficiently is challenging due to the noise present in structure data. Results: In this paper we present a novel approach to elucidate conformational variability in structures solved using X-ray crystallography. We first infer an ensemble to represent the experimental data and then formulate the identification of truly variable members of the ensemble (as opposed to those that vary only due to noise) as a sparse estimation problem. Our results indicate that the algorithm is able to accurately distinguish genuine conformational changes from variability due to nois... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4732571 Mon, 18 Apr 2011 23:00:00 +0100 4732571 http://www.medworm.com/index.php?rid=4663231&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F6 Conclusions: The mining results conducted in this study reveal that WildSpan is efficient and effective in discovering functional signatures of proteins directly from sequences. The proposed pruning strategy is effective in improving the scalability of WildSpan. It is demonstrated in this study that the W-patterns discovered by WildSpan provides useful information in characterizing protein sequences. The WildSpan executable and open source codes are available on the web (http://biominer.csie.cyu.edu.tw/wildspan). (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4663231 Wed, 30 Mar 2011 23:00:00 +0100 4663231 http://www.medworm.com/index.php?rid=4626180&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F5 Conclusions: Experiments on biological datasets prove that the method is effective and much faster than exhaustive enumeration of candidate patterns. Software is available freely by academic users via the web interface at http://bcb.dei.unipd.it:8080/dyweb. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4626180 Wed, 23 Mar 2011 00:00:00 +0100 4626180 http://www.medworm.com/index.php?rid=4565259&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F3 Conclusions: Our algorithm significantly speeds up methods for the prediction of RNA-RNA interactions andother applications that require the accessibility of RNA molecules. The algorithm is already available in theprogram RNAplfold of the ViennaRNA package. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4565259 Wed, 09 Mar 2011 00:00:00 +0100 4565259 http://www.medworm.com/index.php?rid=4348996&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F6%2F1%2F1 Conclusions: In summary, FC with a parameter setting that makes it robust with respect to small and medium-sized datasets, i.e., number of items to cluster in the hundreds and number of conditions up to a thousand, seems to be the internal validation measure of choice. Moreover, the technique we have developed here can be used in other contexts, in particular for the speed-up of stability-based validation measures. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4348996 Fri, 14 Jan 2011 00:00:00 +0100 4348996 http://www.medworm.com/index.php?rid=4301959&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F39 Conclusion: Experimental results on the sparsified Reeder-Giegerich algorithm suggest a linear speedup over the unsparsified implementation. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4301959 Fri, 31 Dec 2010 00:00:00 +0100 4301959 http://www.medworm.com/index.php?rid=4232698&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F37 Conclusions: For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4232698 Mon, 06 Dec 2010 00:00:00 +0100 4232698 http://www.medworm.com/index.php?rid=4162551&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F36 Conclusions: A comprehensive comparative analysis of methodologies for module detection based on modularity maximisation shows that our approach outperforms previously reported methods. Furthermore, in contrast to previous reports, we propose a strategy to handle resolution limitations in modularity maximisation. Overall, we illustrate ways to improve existing methodologies for community structure identification so as to increase its efficiency and applicability. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4162551 Fri, 12 Nov 2010 00:00:00 +0100 4162551 http://www.medworm.com/index.php?rid=4149790&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F35 Conclusions: Our method is able to assess both the evidence of selection at individual amino acid sites and estimate the reliability of those inferences. Experimental validation with I-BmoI proves its utility to identify functionally-important residues of poorly characterized proteins, demonstrating increased sensitivity over previous methods without loss of specificity. With the ability to guide the selection of precise experimental mutagenesis conditions, our method helps make unigenic analysis a more broadly applicable technique with which to probe protein function.AvailabilitySoftware to compute, plot, and summarize EoS data is available as an open-source package called 'unigenic' for the 'R' programming language at (http://www.fernandes.org/txp/article/13/an-analytical-framework-for-u... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4149790 Mon, 08 Nov 2010 00:00:00 +0100 4149790 http://www.medworm.com/index.php?rid=4117039&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F34 Conclusions: As the sensitivity of AP-MS pipeline improves, the fraction of indirect interactions detected will also increase, thereby making the ability to distinguish them even more desirable. Despite the simplicity of our model for indirect interactions, our method provides a good performance on the test networks. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4117039 Thu, 28 Oct 2010 23:00:00 +0100 4117039 http://www.medworm.com/index.php?rid=4039834&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F33 Background: Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT) protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results: We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to mutations. The scoring function captures both sequence and structure information. By exploring the literature, we have ... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=4039834 Wed, 06 Oct 2010 23:00:00 +0100 4039834 http://www.medworm.com/index.php?rid=3986412&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F32 Conclusions: The mathematical proof demonstrates that GFA could be convergent in the global optimum by probability 1 in three conditions for one independent variable mass functions. In addition to these results, the fundamental optimization concept in this paper is used to analyze how SA and GA affect the global search and the inherent defects in SA and GA. Some results and source code (in Matlab) are publicly available at http://ccst.jlu.edu.cn/CSBG/GFA. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3986412 Sun, 19 Sep 2010 23:00:00 +0100 3986412 http://www.medworm.com/index.php?rid=3953261&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F31 Conclusions: The efficiency of the algorithm is demonstrated in situations where standard Fourier-based spectral methods are poorly adapted. We also show how the proposed framework allows to identify the 1's that participate to the periodic trends, i.e. how the framework allows to allocate a positional score to genes, in the same spirit of the sequence score. The software is available for public use at http://www.issb.genopole.fr/MEGA/Softwares/iSSB_SolenoidalApplication.zip (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3953261 Thu, 09 Sep 2010 23:00:00 +0100 3953261 http://www.medworm.com/index.php?rid=3871899&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F30 It has been demonstrated that genes in a cell do not act independently. They interact with one another to complete certain biological processes or to implement certain molecular functions. How to incorporate biological pathways or functional groups into the model and identify survival associated gene pathways is still a challenging problem. In this paper, we propose a novel iterative gradient based method for survival analysis with group Lp penalized global AUC summary maximization. Unlike LASSO, Lp (p (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3871899 Sun, 15 Aug 2010 23:00:00 +0100 3871899 http://www.medworm.com/index.php?rid=3699029&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F28 Conclusions: For small datasets (a few hundred proteins) it is possible to solve the problem to optimality with moderate computational effort using commercial or free solvers. Larger datasets, like full proteomes require the use of heuristics. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3699029 Thu, 24 Jun 2010 23:00:00 +0100 3699029 http://www.medworm.com/index.php?rid=3690384&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F27 Conclusions: The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. Incomparison with RNAinverse it uses new ideas, for instance by considering sets of competing structures. As a result, Inv is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3690384 Tue, 22 Jun 2010 23:00:00 +0100 3690384 http://www.medworm.com/index.php?rid=3644305&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F26 We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure.This structure can be used to develop search methods capable of handling much larger datasets. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3644305 Mon, 07 Jun 2010 23:00:00 +0100 3644305 http://www.medworm.com/index.php?rid=3621008&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F24 Conclusions: AlignMiner can be used to reliably detect divergent regions via several scoring methods that provide different levels of selectivity. Its predictions have been verified by experimental means. Hence, it is expected that its usage will save researchers' time and ensure an objective selection of the best-possible divergent region when closely related sequences are analysed. AlignMiner is freely available at http://www.scbi.uma.es/alignminer. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3621008 Tue, 01 Jun 2010 23:00:00 +0100 3621008 http://www.medworm.com/index.php?rid=3621007&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F25 Conclusions:The algorithms introduced here make it possible to solve the MPP also for large trees with high-degree vertices. This has practical relevance in the field of comparative phylogenetics and, for example, in the context of phylogenetic targeting, i.e., data collection with resource limitations. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3621007 Tue, 01 Jun 2010 23:00:00 +0100 3621007 http://www.medworm.com/index.php?rid=3607031&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F23 Conclusions: Differential co-expression framework is useful to provide quantitative and objective assessment of the goodness of biclusters of co-expressed genes and performance of biclustering algorithms in identifying co-expression biclusters. It also helps to combine the biclusters output by different algorithms into one unified ranking i.e. meta-biclustering. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3607031 Thu, 27 May 2010 23:00:00 +0100 3607031 http://www.medworm.com/index.php?rid=3584950&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F22 We present a novel method that takes compensating base changes across the binding sites into account. The algorithm works in two steps on two pre-generated multiple alignments. In the first step, individual base pairs with high reliability are found using the PETfold algorithm, which includes evolutionary and thermodynamic properties. In step two (where high reliability base pairs from step one are constrained as unpaired), the principle of cofolding is combined with hierarchical folding. The final prediction of intra- and inter-molecular base pairs consists of the reliabilities computed from the constrained expected accuracy scoring, which is an extended version of that used for individual multiple alignments. Results: We derived a rather extensive algorithm. One of the advantages of our ... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3584950 Thu, 20 May 2010 23:00:00 +0100 3584950 http://www.medworm.com/index.php?rid=3563306&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F21 Conclusions: We show how this approach greatly reduces computation time and memory requirements forclustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them asguide trees for multiple alignment. Source code is available for download fromhttp://www.clustal.org/mbed.tgz. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3563306 Thu, 13 May 2010 23:00:00 +0100 3563306 http://www.medworm.com/index.php?rid=3493759&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F20 A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincare, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems Biology. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3493759 Wed, 21 Apr 2010 23:00:00 +0100 3493759 http://www.medworm.com/index.php?rid=3306175&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F18 Conclusions: Our heuristics for the RF supertree problem, based on our new local search algorithms, make it possible for the first time to estimate large supertrees by directly optimizing the RF distance from rooted input trees to the supertrees. This provides a new and fast method to build accurate supertrees. RF supertrees may also be useful for estimating majority-rule(-) supertrees, which are a generalization of majority-rule consensus trees. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3306175 Wed, 24 Feb 2010 00:00:00 +0100 3306175 http://www.medworm.com/index.php?rid=3238965&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F16 Conclusions: The Jane tool is shown to be a useful tool for cophylogenetic reconstruction. Its functionalitycomplements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology,molecular systematics, and biogeography. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3238965 Wed, 03 Feb 2010 00:00:00 +0100 3238965 http://www.medworm.com/index.php?rid=3207833&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F15 Conclusions: Our algorithms prove to be effective and able to handle real data sets with multiple sequences, as well as biological patterns of interest, even when the latter display a high complexity (PROSITE signatures for example). In addition, these exact algorithms allow us to avoid the edge effect observed under the single sequence approximation, which leads to erroneous results, especially when the marginal distribution of the model displays a slow convergence toward the stationary distribution. We end up with a discussion on our method and on its potential improvements. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3207833 Tue, 26 Jan 2010 00:00:00 +0100 3207833 http://www.medworm.com/index.php?rid=3145354&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F14 Background: Accurate classification of microarray data is critical for successful clinical diagnosis and treatment.However, the "curse of dimensionality" problem, and noise in the data undermines the performance of many algorithms.MethodIn order to obtain a robust classifier, a novel Additive Nonparametric Margin Maximum for Case-Based Reasoning (ANMM4CBR) method is proposed in this article. ANMM4CBR employs a case-based reasoning (CBR) method for classification. CBR is a suitable paradigm for microarray analysis, where the rules that definethe domain knowledge are difficult to obtain since usually only a small number of training samples are available. Moreover, in order to select the most informative genes, we propose to perform feature selection via additively optimizing a nonparametric ... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3145354 Wed, 06 Jan 2010 00:00:00 +0100 3145354 http://www.medworm.com/index.php?rid=3138766&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F4 Conclusions: While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3138766 Mon, 04 Jan 2010 00:00:00 +0100 3138766 http://www.medworm.com/index.php?rid=3138765&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F5 Background: Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site. Methods: In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in t... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3138765 Mon, 04 Jan 2010 00:00:00 +0100 3138765 http://www.medworm.com/index.php?rid=3138764&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F6 Conclusions: Our approach allows to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3138764 Mon, 04 Jan 2010 00:00:00 +0100 3138764 http://www.medworm.com/index.php?rid=3138763&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F5%2F1%2F7 Conclusions: Our results show that although the problem of searching for similar structures in a database based on the RMSD measure with indels is NP-hard in the case of unbounded dimensions, it can be solved in 3-D by a simple average-case linear time algorithm when the number of indels is bounded by a constant. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3138763 Mon, 04 Jan 2010 00:00:00 +0100 3138763 http://www.medworm.com/index.php?rid=3133218&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F16 Conclusions: We suggest that our method may be more realisticwhen the relation ancestor-descendant between the analysed genomes is clear and we apply it to do a better characterisation of the evolutionary scenario of the bacterium Rickettsia felis with respect to one of its ancestors. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=3133218 Wed, 30 Dec 2009 00:00:00 +0100 3133218 http://www.medworm.com/index.php?rid=2995294&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F15 Conclusions: The algorithm has been tested on 360 GeneChips from publicly available data of recent expression experiments. The algorithm is fast and accurate. Strong correlations between the fitted values for different experiments as well as between the free-energy parameters and their counterparts in aqueous solution indicate that our model captures a significant part of the underlying physical chemistry. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2995294 Mon, 16 Nov 2009 00:00:00 +0100 2995294 http://www.medworm.com/index.php?rid=2943102&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F14 Conclusion: iTriplet is a novel rule-based combinatorial or enumerative motif finding method that is able to process highly degenerate and long motifs that have resisted analysis by other methods. In addition, iTriplet is distinguished from other methods of the same family by its parallelizability, which allows it to leverage the power of today's readily available high-performance computing systems. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2943102 Thu, 29 Oct 2009 00:00:00 +0100 2943102 http://www.medworm.com/index.php?rid=2908112&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F12 Conclusions: Using our new cluster selection method together with the method by Palla et al. provides a new interesting clustering mechanism that allows to compute overlapping clusters which is especially valuable for biological and chemical data sets. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2908112 Sun, 18 Oct 2009 23:00:00 +0100 2908112 http://www.medworm.com/index.php?rid=2691053&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F11 Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA sequence variation in the genome and they have recently emerged as valuable genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here, we extend an algorithmic model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed differently due to their parental origin. The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from three SNPs, OPRKG36T (with two alleles G and T), OPRKA843G (with alleles... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2691053 Mon, 10 Aug 2009 23:00:00 +0100 2691053 http://www.medworm.com/index.php?rid=2610454&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F10 Background: With the increasing availability of live cell imaging technology,tracking cells and other moving objects in live cell videos has become a major challenge for bioimage informatics. An inherent problem for most cell tracking algorithms is over- or under-segmentation of cells -- many algorithms tend to recognize one cell as several cells or vice versa. Results: We propose to approach this problem through so-called topological alignments, which we apply to address the problemof linking segmentations of two consecutive frames in the videosequence. Starting from the output of a conventional segmentationprocedure, we align pairs of consecutive frames through assigning sets of segments in one frame to sets of segments in the next frame. We achieve this through finding maximum weighted ... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2610454 Wed, 15 Jul 2009 23:00:00 +0100 2610454 http://www.medworm.com/index.php?rid=2504354&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F9 The passion of scientists in interdisciplinary fields to understand living beings gave rise to the field of bioinformatics. These scientists employ a number of methodologies and tools to deal with massive amounts of biological data. Bioinformatics: A Computing Perspective is a comprehensive compilation of biological basics, computational methods, and modern approaches for resolving biological problems well suited to individuals with background education in computer science. In addition, this book provides long-running examples and discussions throughout the text to help students understand complex biological ideas. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2504354 Tue, 23 Jun 2009 23:00:00 +0100 2504354 http://www.medworm.com/index.php?rid=2456139&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F8 We present results in real data showing the eectiveness of e -CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in Saccharomyces cerevisiae in response to heat stress. In particular, the results show the advantage of considering approximate patterns when compared to state of the art methods that require exact matching of gene expression time series.DiscussionThe identication of co-regulated genes, involved in specic biological processes, remains one of the main avenues open to researchers studying gene regulatory networks. The ability of the proposed methodology to eciently identify sets of genes with similar expression patterns is shown to be instrumental in the discovery of relevant biological phenomena, ... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2456139 Thu, 04 Jun 2009 04:00:00 +0100 2456139 http://www.medworm.com/index.php?rid=2356211&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F7 Conclusion: Our results demonstrate that to increase sensitivity, specificity, and reproducibility in microarray analyses, we need to select suitable combinations of preprocessing algorithms and gene ranking methods. We recommend the use of FC-based methods, in particular RP or WAD. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2356211 Wed, 22 Apr 2009 04:00:00 +0100 2356211 http://www.medworm.com/index.php?rid=2283702&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F6 Conclusions: The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2283702 Thu, 19 Mar 2009 04:00:00 +0100 2283702 http://www.medworm.com/index.php?rid=2208828&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F5 Conclusions: A statistically robust and computationally efficient LP-based method for estimating the topology of a large sparse undirected graph from high-dimensional data yields representations of genetic networks that are biologically plausible and useful approximations of the structure of real networks. In the learned LP-SLGN models, genes with high random walk betweenness, a measure of the centrality of a node in a graph, are candidates for interventional studies and hence integrated computational - experimental investigations designed to infer more realistic and sophisticated probabilistic directed graphical model representations of genetic networks. The LP-based solutions of the sparse linear regression problem described here may provide a method for learning the structure of transcr... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2208828 Tue, 24 Feb 2009 05:00:00 +0100 2208828 http://www.medworm.com/index.php?rid=2171734&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F4 Conclusions: Inspired by image processing and the dot plot representation for RNA secondary structure, we have managed to provide a conceptually new and potentially beneficial metric for comparing two RNA secondary structures. We illustrated our approach on the RNA design problem, as well as on an application that utilizes the distance measure to detect conformational rearranging point mutations in an RNA sequence. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2171734 Mon, 09 Feb 2009 05:00:00 +0100 2171734 http://www.medworm.com/index.php?rid=2146707&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F3 Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Finding such fragments while allowing for a certain number of insertions, deletions, and substitutions, is however known to be a computationally expensive task, and consequently exact methods can usually not be applied in practice. The filter Tuiuiu that we introduce in this paper provides a possible solution to this problem. It can be used as a preprocessing step to any multiple alignment or repeats inference method, eliminating a possibly large fraction of the input that is guaranteed not to contain any approximate repeat. It consists in the verification of several st... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2146707 Fri, 30 Jan 2009 05:00:00 +0100 2146707 http://www.medworm.com/index.php?rid=2107010&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F2 Conclusions: CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2107010 Thu, 15 Jan 2009 05:00:00 +0100 2107010 http://www.medworm.com/index.php?rid=2086222&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F4%2F1%2F1 Conclusions: This solves the open problem of rigorously drawing independent and identically distributed samples from the posterior distribution over rooted and unrooted small tree spaces (3 or 4 taxa) based on any multiply-aligned sequence data. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2086222 Wed, 07 Jan 2009 05:00:00 +0100 2086222 http://www.medworm.com/index.php?rid=2058994&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F16 Conclusions: The proposed HuMiTar method constitutes a step towards providing an efficient model for studying translational gene regulation by miRs. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=2058994 Mon, 22 Dec 2008 05:00:00 +0100 2058994 http://www.medworm.com/index.php?rid=1937379&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F14 Conclusions: We propose Syntenator as a software solution to reliably infer conserved syntenies among distantly related genomes. The software is available from http://www2.tuebingen.mpg.de/abt4/plone. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1937379 Thu, 06 Nov 2008 05:00:00 +0100 1937379 http://www.medworm.com/index.php?rid=1937378&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F15 Conclusions: ``One-out strategies'', known to be a useful tool for testing the stability of all sorts of data-analysis procedures, can successfully be used also in testing alignment stability. In case instabilities are observed, the sequences under consideration should be carefully checked for putative causes. In case one suspects sequence repeats to be the cause, the new ``sc'' option can be used to detect such repeats, and the ``xfr'' option can help to resolve the resulting problems. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1937378 Thu, 06 Nov 2008 05:00:00 +0100 1937378 http://www.medworm.com/index.php?rid=1913787&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F13 The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reconstruction. Such needs are hardly fulfilled by the more traditional measures of sequence similarity and distance, like string edit and gene rearrangement, due to a mixture of epistemological and computational problems. Alternative measures, based on the subword composition of sequences, have emerged in recent years and proved to be both fast and effective in a variety of tested cases. The common denominator of such measures is an underlying information theoretic notion of relative compressibility. Their viability depends critically on computational cost. The present paper describes as a paradigm the extension and ... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1913787 Tue, 28 Oct 2008 04:00:00 +0100 1913787 http://www.medworm.com/index.php?rid=1741625&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F11 Conclusion: The single-chip based hook-method provides accurate expression estimates and chip-summary characteristics using the natural metrics given by the hybridization reaction with the potency to develop new standards for microarray quality control and calibration. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1741625 Fri, 29 Aug 2008 04:00:00 +0100 1741625 http://www.medworm.com/index.php?rid=1741624&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F12 Conclusions: The hook-method corrects the raw intensities for the non-specific background hybridization in a sequence-specific manner, for the potential saturation of the probe-spots with bound transcripts and for the sequence-specific binding of specific transcripts. The obtained chip characteristics in combination with the sensitivity corrected probe-intensity values provide expression estimates scaled in natural units which are given by the binding constants of the particular hybridization. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1741624 Fri, 29 Aug 2008 04:00:00 +0100 1741624 http://www.medworm.com/index.php?rid=1634128&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F10 Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1634128 Thu, 17 Jul 2008 04:00:00 +0100 1634128 http://www.medworm.com/index.php?rid=1546178&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F8 Conclusion: WAD is a promising alternative to existing methods for ranking DEGs with two classes. Its high performance should increase researchers' confidence in microarray analyses. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1546178 Thu, 26 Jun 2008 04:00:00 +0100 1546178 http://www.medworm.com/index.php?rid=1546177&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F9 Conclusions: Our specialized realization of self-organizing maps is well-suitable to gain insight into complex pattern variation in a large set of metabolite profiles. In comparison to other methods our visualization approach facilitates the identification of interesting groups of metabolites by means of a convenient overview on relevant intensity patterns. In particular, the visualization effectively supports researchers in analyzing many putative clusters when the true number of biologically meaningful groups is unknown. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1546177 Thu, 26 Jun 2008 04:00:00 +0100 1546177 http://www.medworm.com/index.php?rid=1541219&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F7 We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of ``tree quality''. In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software: The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignme... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1541219 Tue, 24 Jun 2008 04:00:00 +0100 1541219 http://www.medworm.com/index.php?rid=1468694&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F6 Conclusion: On BALIBASE3, our new program performs significantly better than the previous program DIALIGN-T and outperforms the popular global aligner CLUSTAL W, though it is still outperformed by programs that focus on global alignment like MAFFT, MUSCLE and T-COFFEE. On the locally related test sets in IRMBASE 2 and DIRMBASE 1, our method outperforms all other programs while MAFFT E-INSi is the only method that comes close to the performance of DIALIGN-TX. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1468694 Tue, 27 May 2008 04:00:00 +0100 1468694 http://www.medworm.com/index.php?rid=1409197&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F5 The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is "optimal" when the algorithm outputs the tree which minimizes the balanced minimum evolution criterion. We use the fact that the NJ tree topology and the BME tree topology are determined by polyhedral subdivisions of the spaces of dissimilarity maps IR_{+}^{n \choose 2} to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for n less than or equal to 8. A key requirement is the measurement of volumes of spherical polytopes in high dimension, which we obtain using a combination of Monte Carlo methods and polyhedr... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1409197 Wed, 30 Apr 2008 04:00:00 +0100 1409197 http://www.medworm.com/index.php?rid=1343073&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F4 Conclusions: The probabilistic framework has an elegance in principle, merging sequence and structure descriptors into a single framework. It has a practical use in fast structural alignments and a potential use in finding those examples where sequence and structural similarities apparently disagree. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1343073 Tue, 01 Apr 2008 04:00:00 +0100 1343073 http://www.medworm.com/index.php?rid=1339635&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F3 Conclusions: We show that SBM can be applied to target prediction in both plants and animals and performs well in terms of sensitivity and specificity. Open source code implementing the SBM method, together with documentation and examples are freely available for download from http://www.cmp.uea.ac.uk/~jtk/stackbm/ (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1339635 Mon, 31 Mar 2008 04:00:00 +0100 1339635 http://www.medworm.com/index.php?rid=1182497&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F2 Conclusions: One and two class methods can both give useful classification accuracies when the negative class is well characterized. The advantage of one class methods is that it eliminates guessing at the optimal features for the negative class when they are not well defined. In these cases one-class methods can be superior to two-class methods when the features which are chosen as representative of that positive class are well defined.AvailabilityThe OneClassmiRNA program is available at: [1] (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1182497 Mon, 28 Jan 2008 05:00:00 +0100 1182497 http://www.medworm.com/index.php?rid=1174601&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F3%2F1%2F1 Conclusions: The three proposed algorithms are mathematically guaranteed to reconstruct the ``true'' phylogeny with a high success probability. The experimental results showed that the third algorithm produced phylogenies with a higher probability than its aforementioned theoretical lower bound and outperformed some existing phylogeny reconstruction methods in both speed and accuracy. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1174601 Thu, 24 Jan 2008 05:00:00 +0100 1174601 http://www.medworm.com/index.php?rid=1114683&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F16 Conclusions: In this work we have surveyed and categorized 14 significance measures for pattern evaluation. Their ability to rank three types of deterministic motifs was evaluated. Measures were applied in different testing conditions, where relations were identified. This study provides some pertinent insights on the choice of the right set of significance measures for the evaluation of deterministic motifs extracted from protein databases. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1114683 Mon, 24 Dec 2007 05:00:00 +0100 1114683 http://www.medworm.com/index.php?rid=1087087&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F15 Conclusions: We have tested TFM-Pvalue on a large set of PWMs representing transcription factor binding sites. Experimental results show that it achieves better performance in terms of computational time and precision than existing tools. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1087087 Tue, 11 Dec 2007 05:00:00 +0100 1087087 http://www.medworm.com/index.php?rid=1006645&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F14 no abstract for this type of article (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=1006645 Tue, 06 Nov 2007 05:00:00 +0100 1006645 http://www.medworm.com/index.php?rid=939558&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F13 Conclusions: The primary objective of the program is to assess the likelihood that a given DNA segment is CRM regulated with a known set of regulatory factors. In addition, the program can also be used to select the appropriate threshold for PWM scanning. Another application is assessing similarity of different motifs.AvailabilityProject web page, stand-alone version and documentation can be found at http://bioinform.genetika.ru/AhoPro/ (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=939558 Wed, 10 Oct 2007 04:00:00 +0100 939558 http://www.medworm.com/index.php?rid=924680&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F12 Conclusions: Our best method (Row and Column Weighed Mutual Information) has an estimated accuracy increase of 63% over Mutual Information. Furthermore, we show that the combination of different methods is efficient, and that the methods are quite sensitive to the different conditions tested. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=924680 Wed, 03 Oct 2007 04:00:00 +0100 924680 http://www.medworm.com/index.php?rid=884979&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F11 We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O(|s|.|t|.N) using O(|s|+|t|.N) memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distribu... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=884979 Wed, 19 Sep 2007 04:00:00 +0100 884979 http://www.medworm.com/index.php?rid=881458&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F10 This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for t... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=881458 Tue, 18 Sep 2007 04:00:00 +0100 881458 http://www.medworm.com/index.php?rid=728009&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F9 Conclusions: Our results show that the statistics of gapped and ungapped local alignments deviates significantly from Gumbel in the rare-event tail. We provide a Gaussian correction to the distribution and an analysis of its scaling behavior for several different scoring parameter sets, which are commonly used to search protein data bases. The case of sum statistics of k best alignments is included. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=728009 Wed, 11 Jul 2007 04:00:00 +0100 728009 http://www.medworm.com/index.php?rid=701664&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F8 Background: Neighbor-Net is a novel method for phylogenetic analysis that is currently being widely used in areas such as virology, bacteriology, and plant evolution. Given an input distance matrix, Neighbor-Net produces a phylogenetic network, a generalization of an evolutionary or phylogenetic tree which allows the graphical representation of conflicting phylogenetic signals. Results: In general, any network construction method should not depict more conflict than is found in the data, and, when the data is fitted well by a tree, the method should return a network that is close to this tree. In this paper we provide a formal proof that Neighbor-Net satisfies both of these requirements so that, in particular, Neighbor-Net is statistically consistent on circular distances. (Source: Algori... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=701664 Thu, 28 Jun 2007 04:00:00 +0100 701664 http://www.medworm.com/index.php?rid=655205&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F7 Conclusions: The findings have been achieved based on analytical evaluations, not empirical evaluation involving classifiers, thus providing further basis for the usefulness of the DDP and validating the need for unequal priorities on relevance and redundancy during feature selection for microarray datasets, especially highly multiclass datasets. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=655205 Mon, 04 Jun 2007 04:00:00 +0100 655205 http://www.medworm.com/index.php?rid=647074&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F6 We present here a support vector machine (SVM) that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment and provides a dramatic improvement in classification accuracy over previous approaches. Software: RNAstrand is freely available as a stand-alone tool from http://www.bioinf.uni-leipzig.de/Software/ and it is also included in the latest release of RNAz, a part of the Vienna RNA Package. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=647074 Thu, 31 May 2007 04:00:00 +0100 647074 http://www.medworm.com/index.php?rid=643187&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F5 Conclusion: GOGOT is useful for the automated detection of differentially expressed TDFs from cDNA-AFLP temporal electrophoretic data. The current algorithm may be applied to other electrophoretic data and temporal microarray data. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=643187 Wed, 30 May 2007 04:00:00 +0100 643187 http://www.medworm.com/index.php?rid=540505&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F4 This is a meeting report for the 6th SIGKDD Workshop on Data Mining in Bioinformatics. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=540505 Wed, 11 Apr 2007 04:00:00 +0100 540505 http://www.medworm.com/index.php?rid=520512&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F3 Understanding the protein folding mechanism remains a grand challenge in structural biology. In the past several years, computational theories in molecular dynamics have been employed to shed light on the folding process. Coupled with high computing power and large scale storage, researchers now can omputationally simulate the protein folding process in atomistic details at femtosecond temporal resolution. Such simulation often produces a large number of folding trajectories, each consisting of a series of 3D conformations of the protein under study. As a result, effectively managing and analyzing such trajectories is becoming increasingly important. In this article, we present a spatio-temporal mining approach to analyze protein folding trajectories. It exploits the simplicity of contact ... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=520512 Wed, 04 Apr 2007 04:00:00 +0100 520512 http://www.medworm.com/index.php?rid=512485&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F2 Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. We develop a methodology, TRND, that integrates a preliminary TRN, microarray data, gene ontology and phylogenic similarity to accurately discover TRNs and apply the method to E.coli K12. The approach can easily be extended to include other methodologies. Although gene ontology and phylogenic similarity have been used in the context of gene-gene networks, we show that more information can be extracted when gene-gene scores are transformed to gene-transcription factor (TF) scores using a preliminary TRN. This seems to be preferable over th... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=512485 Fri, 30 Mar 2007 04:00:00 +0100 512485 http://www.medworm.com/index.php?rid=375574&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F2%2F1%2F1 Conclusions: Better sensitivity and specificity can be achieved through a combination of (1) using mixed alignable and non-alignable sequence data and (2) combining evidence from multiple sites within an intergenic region. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=375574 Tue, 23 Jan 2007 07:00:00 +0100 375574 http://www.medworm.com/index.php?rid=314983&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F25 Conclusions: When implemented, the AB and TFB methods give equivalent results in a variety of situations relevant to biology. Overall, the Smoluchowski method as modified by Andrews and Bray emerges as the most simple, robust and efficient method for simulating biological diffusion-reaction processes of individual molecules currently available. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=314983 Mon, 11 Dec 2006 07:00:00 +0100 314983 http://www.medworm.com/index.php?rid=308146&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F24 The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clustering and detecting functional modules in protein-protein interaction networks, termed STM. STM selects representative proteins for each cluster and iteratively refines clusters based on a combination of the signal transduced and graph topology. STM is found to be effective at detecting clusters with a diverse range of interaction structures that are significant on measures of biological relevance. The STM approach is compared to six competing approaches including the maximum clique, quasi-clique, minimum cut, betweeness cut and Markov Clustering (MCL) algorithms. The clusters obtai... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=308146 Tue, 05 Dec 2006 07:00:00 +0100 308146 http://www.medworm.com/index.php?rid=441186&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F24 Conclusion: STM outperforms competing approaches and is capable of effectively detecting both densely and sparsely connected, biologically relevant functional modules with fewer discards. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=441186 Tue, 05 Dec 2006 05:00:00 +0100 441186 http://www.medworm.com/index.php?rid=290880&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F23 The main goal of the motif finding problem is to detect novel, over-represented unknown signals in a set of sequences (e.g. transcription factor binding sites in a genome). The most widely used algorithms for finding motifs obtain a generative probabilistic representation of these over-represented signals and try to discover profiles that maximize the information content score. Although these profiles form a very powerful representation of the signals, the major difficulty arises from the fact that the best motif corresponds to the global maximum of a non-convex continuous function. Popular algorithms like Expectation Maximization (EM) and Gibbs sampling tend to be very sensitive to the initial guesses and are known to converge to the nearest local maximum very quickly. In order to improve... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=290880 Mon, 27 Nov 2006 07:00:00 +0100 290880 http://www.medworm.com/index.php?rid=284392&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F22 Conclusions: sMOTIF is a useful and efficient tool in searching for structured pattern and profile motifs. The algorithm is available as open-source at: http://www.cs.rpi.edu/~zaki/software/sMotif/. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=284392 Tue, 21 Nov 2006 07:00:00 +0100 284392 http://www.medworm.com/index.php?rid=278457&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F21 Conclusions: ExMotif is a useful and efficient tool in discovering structured motifs, especially in DNA sequences. The algorithm is available as open-source at: http://www.cs.rpi.edu/~zaki/software/exMotif/. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=278457 Thu, 16 Nov 2006 07:00:00 +0100 278457 http://www.medworm.com/index.php?rid=251729&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F20 Background: A new, promising solvent exposure measure, called half-sphere-exposure (HSE), has recently been proposed. Here, we study the reconstruction of a proteins C-alpha trace solely from structure-derived HSE information. This problem is of relevance for de novo structure prediction using predicted HSE measure. For comparison, we also consider the well-established contact number (CN) measure. We define energy functions based on the HSE- or CN-vectors and minimize them using two conformational search heuristics: Monte Carlo simulation (MCS) and tabu search (TS). While MCS has been the dominant conformational search heuristic in literature, TS has been applied only a few times. To discretize the conformational space, we use lattice models with various complexity. Results: The proposed T... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=251729 Fri, 27 Oct 2006 06:00:00 +0100 251729 http://www.medworm.com/index.php?rid=239841&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F18 In this study a family of kernel density functions is described that accommodates the fractal nature of iterative function representations of symbolic sequences and, consequently, enables the exact investigation of sequence motifs of arbitrary lengths in that scale-independent representation. Furthermore, the proposed kernel density includes both Markovian succession and currently used alignment-free sequence dissimilarity metrics as special solutions. Therefore, the fractal kernel described is in fact a generalization that provides a common framework for a diverse suite of sequence analysis techniques. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=239841 Wed, 18 Oct 2006 06:00:00 +0100 239841 http://www.medworm.com/index.php?rid=239842&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F17 Conclusions: We establish that the use of high order Markov model could easily lead to major mistakes due to the high sensitivity of pattern statistics to parameter estimation. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=239842 Tue, 17 Oct 2006 06:00:00 +0100 239842 http://www.medworm.com/index.php?rid=204489&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F16 Conclusions: We present a new algorithm for computing the quartet distance between two trees of arbitrary degree. The new algorithm improves the asymptotic running time for computing the quartet distance, compared to previous methods, and experimental results indicate that the new method also performs significantly better in practice. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=204489 Mon, 25 Sep 2006 06:00:00 +0100 204489 http://www.medworm.com/index.php?rid=173520&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F15 Conclusions: We demonstrate the usefulness of our approach on gene expression data for two types of leukaemia and on protein-DNA binding data for two growth conditions in Saccharomyces cerevisiae. The software implementing the layout algorithm is available at http://bioinformatics.cs.vt.edu/~murali/papers/bivoc. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=173520 Mon, 04 Sep 2006 06:00:00 +0100 173520 http://www.medworm.com/index.php?rid=156678&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F14 Conclusions: ExAlt identifies the structure of most alternatively spliced exons in the test set and cross-species sequence conservation is shown to improve the precision of predictions. The software package is available to run on Drosophila genomes to search for new cases of alternative splicing. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=156678 Fri, 25 Aug 2006 06:00:00 +0100 156678 http://www.medworm.com/index.php?rid=148654&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F13 Conclusions: Our results demonstrate that a combined graph theoretic and mathematical programming approach can be the basis for effective and powerful techniques for diverse motif finding applications. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=148654 Thu, 17 Aug 2006 06:00:00 +0100 148654 http://www.medworm.com/index.php?rid=140303&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F12 The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses) through the result of the hybridization experiment. In this paper we show that SBC is as hard to approximate as Set Cover. Furthermore, we show that the constrained version of SBC (with probes of bounded length) is also hard to approximate. These negative results are tight. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=140303 Tue, 08 Aug 2006 06:00:00 +0100 140303 http://www.medworm.com/index.php?rid=96277&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F7 Conclusion: The proposed representation helps in understanding the transitions between functional groups and allows for tracking a protein's path through a cascade of functional groups. Therefore, depending on the nature of the network, our representation is capable of elucidating temporal relations between functional groups. Our results show that the proposed method opens a new avenue for the analysis of protein interaction networks. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=96277 Wed, 26 Apr 2006 06:00:00 +0100 96277 http://www.medworm.com/index.php?rid=96278&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F6 Background: Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results: Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we app... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=96278 Wed, 19 Apr 2006 06:00:00 +0100 96278 http://www.medworm.com/index.php?rid=96279&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F5 In this study, the asymptotic approximations appear to be completely unreliable for 99.5% of the considered sequences. Concerning the pattern statistics, the new FMCI algorithms dramatically outperform the previous ones as they are more reliable, easier to implement, faster and with lower memory requirements. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=96279 Fri, 07 Apr 2006 06:00:00 +0100 96279 http://www.medworm.com/index.php?rid=96280&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F4 Conclusion: Off-line compression based on extensible motifs can be used advantageously to compress and classify biological sequences. (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=96280 Thu, 23 Mar 2006 07:00:00 +0100 96280 http://www.medworm.com/index.php?rid=96281&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F3 We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.AvailabilityRNAcofold is distributed as part of the Vienna RNA Package, http://www.tbi.univie.ac.at/RNA/.ContactStephan H. Bernhart – berni@tbi.univie.ac.at (Source: Algorithms for Molecular Bio... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=96281 Thu, 16 Mar 2006 07:00:00 +0100 96281 http://www.medworm.com/index.php?rid=96283&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F1 This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a forum for fast publication of high-quality research articles in this rapidly evolving field. Our journal will publish thoroughly peer-reviewed papers without length limitations covering all aspects of algorithmic data analysis in computatioal biology. Publications in Algorithms for Molecular Biology are easy to find, highly visible and tracked by organisations such as PubMed. An established online submission system makes a fast reviewing procedure possible and enables us to publish accepted papers without delay. All articles published in our journal are permanently archived by PubMed C... Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=96283 Tue, 28 Feb 2006 07:00:00 +0100 96283 http://www.medworm.com/index.php?rid=96282&cid=s_30456_67_f&fid=30456&url=http%3A%2F%2Fwww.almob.org%2Fcontent%2F1%2F1%2F2 SummaryThe genomes of many species are dominated by short sequences repeated consecutively. It is estimated that over 10% of the human genome consists of tandemly repeated sequences. Finding repeated regions in long sequences is important in sequence analysis.We develop a software, LocRepeat, that finds regions of pseudo-periodic repeats in a long sequence. We use the definition of Li et al. 1 for the pseudo-periodic partition of a region and extend the algorithm that can select the repeated region from a given long sequence and give the pseudo-periodic partition of the region.AvailabilityLocRepeat is available at http://www.cs.cityu.edu.hk/~lwang/software/LocRepeat (Source: Algorithms for Molecular Biology) Algorithms for Molecular Biology journals http://www.medworm.com/rss/comments.php?id=96282 Tue, 28 Feb 2006 07:00:00 +0100 96282