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Linear model for fast background subtraction in oligonucleotide microarrays.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19917117 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - November 16, 2009 Category: Molecular Biology Authors: Kroll KM, Barkema GT, Carlon E Tags: Algorithms Mol Biol Source Type: journals

iTriplet, a rule-based nucleic acid sequence motif finder.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19874606 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - October 29, 2009 Category: Molecular Biology Authors: Ho ES, Jakubowski CD, Gunderson SI Tags: Algorithms Mol Biol Source Type: journals

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics Applications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: We show that in a typical biosequence labeling problem the GRHCRF performs better than CRF models of the same complexity, indicating that GRHCRFs can be useful tools for biosequence analysis applications. AVAILABILITY: GRHCRF software is available under GPLv3 licence at the website http://www.biocomp.unibo.it/ savojard/biocrf-0.9.tar.gz. PMID: 19849839 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - October 22, 2009 Category: Molecular Biology Authors: Fariselli P, Savojardo C, Martelli PL, Casadio R Tags: Algorithms Mol Biol Source Type: journals

Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methods.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19840391 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - October 18, 2009 Category: Molecular Biology Authors: Zahoranszky LA, Katona GY, Hari P, Malnasi-Csizmadia A, Zweig KA, Zahoranszky-Kohalmi G Tags: Algorithms Mol Biol Source Type: journals

Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: 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...
Source: Algorithms for Molecular Biology : AMB - August 10, 2009 Category: Molecular Biology Authors: Wen S, Wang C, Berg A, Li Y, Chang MM, Filligim RB, Wallace MR, Staud R, Kaplan L, Wu R Tags: Algorithms Mol Biol Source Type: journals

Tracking cells in Life Cell Imaging videos using topological alignments.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: 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 problem of linking segmentations of two consecutive frames in the video sequence. Starting from the output of a conventional segmentat...
Source: Algorithms for Molecular Biology : AMB - July 15, 2009 Category: Molecular Biology Authors: Mosig A, Jager S, Wang C, Nath S, Ersoy I, Palaniappan K, Chen SS Tags: Algorithms Mol Biol Source Type: journals

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19386098 [PubMed - in process] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - June 12, 2009 Category: Molecular Biology Authors: Kadota K, Nakai Y, Shimizu K Tags: Algorithms Mol Biol Source Type: journals

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. DISCUSSION: The 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...
Source: Algorithms for Molecular Biology : AMB - June 4, 2009 Category: Molecular Biology Authors: Madeira SC, Oliveira AL Tags: Algorithms Mol Biol Source Type: journals

Evolving DNA motifs to predict GeneChip probe performance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19298675 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - March 19, 2009 Category: Molecular Biology Authors: Langdon WB, Harrison AP Tags: Algorithms Mol Biol Source Type: journals

A Linear Programming Approach for estimating the structure of a Sparse Linear Genetic Network from transcript profiling data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 rep...
Source: Algorithms for Molecular Biology : AMB - February 24, 2009 Category: Molecular Biology Authors: Bhadra S, Bhattacharyya C, Chandra NR, Mian IS Tags: Algorithms Mol Biol Source Type: journals

An image processing approach to computing distances between RNA secondary structures dot plots.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19203377 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - February 9, 2009 Category: Molecular Biology Authors: Ivry T, Michal S, Avihoo A, Sapiro G, Barash D Tags: Algorithms Mol Biol Source Type: journals

Lossless filter for multiple repeats with bounded edit distance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: 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...
Source: Algorithms for Molecular Biology : AMB - January 30, 2009 Category: Molecular Biology Authors: Peterlongo P, Sacomoto GA, Pereira do Lago A, Pisanti N, Sagot MF Tags: Algorithms Mol Biol Source Type: journals

CHSMiner: a GUI tool to identify chromosomal homologous segments.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19146671 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 15, 2009 Category: Molecular Biology Authors: Wang Z, Ding G, Yu Z, Liu L, Li Y Tags: Algorithms Mol Biol Source Type: journals

Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19128477 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 7, 2009 Category: Molecular Biology Authors: Sainudiin R, York T Tags: Algorithms Mol Biol Source Type: journals

HuMiTar: A sequence-based method for prediction of human microRNA targets.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSIONS: The proposed HuMiTar method constitutes a step towards providing an efficient model for studying translational gene regulation by miRs. PMID: 19102780 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - December 22, 2008 Category: Molecular Biology Authors: Ruan J, Chen H, Kurgan L, Chen K, Kang C, Pu P Tags: Algorithms Mol Biol Source Type: journals

Syntenator: Multiple gene order alignments with a gene-specific scoring function.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18990215 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - November 6, 2008 Category: Molecular Biology Authors: Rodelsperger C, Dieterich C Tags: Algorithms Mol Biol Source Type: journals

Stability of Multiple Alignments and Phylogenetic Trees: An Analysis of ABC-Transporter Proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18990223 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - November 6, 2008 Category: Molecular Biology Authors: Dress AW, Morgenstern B, Wagner H Tags: Algorithms Mol Biol Source Type: journals

Fast Algorithms for Computing Sequence Distances by Exhaustive Substring Composition.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: 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 und...
Source: Algorithms for Molecular Biology : AMB - October 28, 2008 Category: Molecular Biology Authors: Apostolico A, Denas O Tags: Algorithms Mol Biol Source Type: journals

"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18759984 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - August 29, 2008 Category: Molecular Biology Authors: Binder H, Krohn K, Preibisch S Tags: Algorithms Mol Biol Source Type: journals

"Hook"-calibration of GeneChip-microarrays: Theory and algorithm.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18759985 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - August 29, 2008 Category: Molecular Biology Authors: Binder H, Preibisch S Tags: Algorithms Mol Biol Source Type: journals

A stitch in time: Efficient computation of genomic DNA melting bubbles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18637171 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - July 17, 2008 Category: Molecular Biology Authors: Tostesen E Tags: Algorithms Mol Biol Source Type: journals

A weighted average difference method for detecting differentially expressed genes from microarray data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18578891 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - June 26, 2008 Category: Molecular Biology Authors: Kadota K, Nakai Y, Shimizu K Tags: Algorithms Mol Biol Source Type: journals

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18582365 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - June 26, 2008 Category: Molecular Biology Authors: Meinicke P, Lingner T, Kaever A, Feussner K, Gobel C, Feussner I, Karlovsky P, Morgenstern B Tags: Algorithms Mol Biol Source Type: journals

Noisy: identification of problematic columns in multiple sequence alignments.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 employe...
Source: Algorithms for Molecular Biology : AMB - June 24, 2008 Category: Molecular Biology Authors: Dress AW, Flamm C, Fritzsch G, Grunewald S, Kruspe M, Prohaska SJ, Stadler PF Tags: Algorithms Mol Biol Source Type: journals

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18505568 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - May 27, 2008 Category: Molecular Biology Authors: Subramanian AR, Kaufmann M, Morgenstern B Tags: Algorithms Mol Biol Source Type: journals

On the optimality of the neighbor-joining algorithm.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: 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 le...
Source: Algorithms for Molecular Biology : AMB - April 30, 2008 Category: Molecular Biology Authors: Eickmeyer K, Huggins P, Pachter L, Yoshida R Tags: Algorithms Mol Biol Source Type: journals

Protein sequence and structure alignments within one framework.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18380904 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - April 1, 2008 Category: Molecular Biology Authors: Schenk G, Margraf T, Torda AE Tags: Algorithms Mol Biol Source Type: journals

A scoring matrix approach to detecting miRNA target sites.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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/ PMID: 18377655 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - March 31, 2008 Category: Molecular Biology Authors: Moxon S, Moulton V, Kim JT Tags: Algorithms Mol Biol Source Type: journals

Learning from positive examples when the negative class is undetermined- microRNA gene identification.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: 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. AVAILABILITY: The OneClassmiRNA program is available at: 1. PMID: 18226233 [PubMed - in process] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - March 3, 2008 Category: Molecular Biology Authors: Yousef M, Jung S, Showe LC, Showe MK Tags: Algorithms Mol Biol Source Type: journals

Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18218120 [PubMed - as supplied by publisher] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 24, 2008 Category: Molecular Biology Authors: Wu G, Kao MY, Lin G, You JH Tags: Algorithms Mol Biol Source Type: journals

PhyloScan: identification of transcription factor binding sites using cross-species evidence.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: 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. PMID: 17244358 [PubMed] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Carmack CS, McCue LA, Newberg LA, Lawrence CE Tags: Algorithms Mol Biol Source Type: journals

Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 tha...
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Sun J, Tuncay K, Haidar AA, Ensman L, Stanley F, Trelinski M, Ortoleva P Tags: Algorithms Mol Biol Source Type: journals

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 computationally 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...
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Yang H, Parthasarathy S, Ucar D Tags: Algorithms Mol Biol Source Type: journals

Data Mining in Bioinformatics (BIOKDD).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 17428327 [PubMed] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Zaki MJ, Karypis G, Yang J Tags: Algorithms Mol Biol Source Type: journals

GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 17535446 [PubMed] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Kadota K, Araki R, Nakai Y, Abe M Tags: Algorithms Mol Biol Source Type: journals

RNAstrand: reading direction of structured RNAs in multiple sequence alignments.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present here a support vector machine that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment and provides a considerable 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/RNAstrand and is also included in the latest release of RNAz, a part of the Vienna RNA Package. PMID: 17540014 [PubMed] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Reiche K, Stadler PF Tags: Algorithms Mol Biol Source Type: journals

Characteristics of predictor sets found using differential prioritization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: 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. PMID: 17547742 [PubMed] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Ooi CH, Chetty M, Teng SW Tags: Algorithms Mol Biol Source Type: journals

Consistency of the neighbor-net algorithm.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Bryant D, Moulton V, Spillner A Tags: Algorithms Mol Biol Source Type: journals

Local sequence alignments statistics: deviations from Gumbel statistics in the rare-event tail.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: 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. PMID: 17625018 [PubMed] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Wolfsheimer S, Burghardt B, Hartmann AK Tags: Algorithms Mol Biol Source Type: journals

A basic analysis toolkit for biological sequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT: 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....
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Giancarlo R, Siragusa A, Siragusa E, Utro F Tags: Algorithms Mol Biol Source Type: journals

Mapping sequences by parts.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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| x |t| x N) using O (|s| x |t| x N) memory space. Among all the numbers o...
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Didier G, Guziolowski C Tags: Algorithms Mol Biol Source Type: journals

Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: 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. PMID: 17915013 [PubMed - in process] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Gouveia-Oliveira R, Pedersen AG Tags: Algorithms Mol Biol Source Type: journals

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: 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. AVAILABILITY: Project web page, stand-alone version and documentation can be found at http://bioinform.genetika.ru/AhoPro/ PMID: 17927813 [PubMed - in process] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Boeva V, Clément J, Régnier M, Roytberg MA, Makeev VJ Tags: Algorithms Mol Biol Source Type: journals

Efficient and accurate P-value computation for Position Weight Matrices.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: 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. PMID: 18072973 [PubMed - in process] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Touzet H, Varré JS Tags: Algorithms Mol Biol Source Type: journals

Evaluating deterministic motif significance measures in protein databases.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
CONCLUSION: 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. PMID: 18157916 [PubMed - in process] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2007 Category: Molecular Biology Authors: Ferreira PG, Azevedo PJ Tags: Algorithms Mol Biol Source Type: journals

Finding the region of pseudo-periodic tandem repeats in biological sequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The 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. PMID: 16722520 [PubMed] (Source: Algorithms...
Source: Algorithms for Molecular Biology : AMB - January 1, 2006 Category: Molecular Biology Authors: Liu X, Wang L Tags: Algorithms Mol Biol Source Type: journals

Effective p-value computations using Finite Markov Chain Imbedding (FMCI): application to local score and to pattern statistics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 16722531 [PubMed - in process] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2006 Category: Molecular Biology Authors: Nuel G Tags: Algorithms Mol Biol Source Type: journals

Multiple sequence alignment with user-defined anchor points.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ABSTRACT : 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, o...
Source: Algorithms for Molecular Biology : AMB - January 1, 2006 Category: Molecular Biology Authors: Morgenstern B, Prohaska SJ, Pöhler D, Stadler PF Tags: Algorithms Mol Biol Source Type: journals

Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 16722537 [PubMed - in process] (Source: Algorithms for Molecular Biology : AMB)
Source: Algorithms for Molecular Biology : AMB - January 1, 2006 Category: Molecular Biology Authors: Zotenko E, Guimarães KS, Jothi R, Przytycka TM Tags: Algorithms Mol Biol Source Type: journals

Analysis of computational approaches for motif discovery.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recently, we performed an assessment of 13 popular computational tools for discovery of transcription factor binding sites (M. Tompa, N. Li, et al., "Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites", Nature Biotechnology, Jan. 2005). This paper contains follow-up analysis of the assessment results, and raises and discusses some important issues concerning the state of the art in motif discovery methods: 1. We categorize the objective functions used by existing tools, and design experiments to evaluate whether any of these objective functions is the right one to optimize. 2. We exam...
Source: Algorithms for Molecular Biology : AMB - January 1, 2006 Category: Molecular Biology Authors: Li N, Tompa M Tags: Algorithms Mol Biol Source Type: journals