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Linear model for fast background subtraction in oligonucleotide microarraysEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - November 16, 2009 Category: Molecular Biology Authors: K Myriam KrollGerard BarkemaEnrico Carlon Source Type: journals

iTriplet, a rule-based nucleic acid sequence motif finderEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - October 29, 2009 Category: Molecular Biology Authors: Eric HoChristopher JakubowskiSamuel Gunderson Source Type: journals

Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methodsEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - October 18, 2009 Category: Molecular Biology Authors: Laszlo ZahoranszkyGyula KatonaPeter HariAndras Malnasi-CsizmadiaKatharina ZweigGergely Zahoranszky-Kohalmi Source Type: journals

Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 analy...
Source: Algorithms for Molecular Biology - August 10, 2009 Category: Molecular Biology Authors: Sheron WenChenguang WangArthur BergYao LiMyron ChangRoger FilligimMargaret WallaceRoland StaudLee KaplanRongling Wu Source Type: journals

Tracking cells in Life Cell Imaging videos using topological alignmentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Algorithms for Molecular Biology - July 15, 2009 Category: Molecular Biology Authors: Axel MosigStefan JagerChaofeng WangSumit NathIlker ErsoyKannappan PalaniappanSu-Shing Chen Source Type: journals

Review of Bioinformatics: A Computing Perspective edited by Shuba Gopal, Anne Haake, Rhys Price Jones and Paul TymannEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Algorithms for Molecular Biology - June 23, 2009 Category: Molecular Biology Authors: Dae-Won KimHong-Seog Park Source Type: journals

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time seriesEmail 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.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 th...
Source: Algorithms for Molecular Biology - June 4, 2009 Category: Molecular Biology Authors: Sara MadeiraArlindo Oliveira Source Type: journals

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificityEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - April 22, 2009 Category: Molecular Biology Authors: Koji Kadota, Yuji Nakai and Kentaro Shimizu Source Type: journals

Evolving DNA motifs to predict GeneChip probe performanceEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - March 19, 2009 Category: Molecular Biology Authors: W B Langdon and A P Harrison Source Type: journals

A Linear Programming Approach for estimating the structure of a Sparse Linear Genetic Network from transcript profiling dataEmail 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 - February 24, 2009 Category: Molecular Biology Authors: Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma R. Chandra and I. Saira Mian Source Type: journals

An image processing approach to computing distances between RNA secondary structures dot plotsEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - February 9, 2009 Category: Molecular Biology Authors: Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro and Danny Barash Source Type: journals

Lossless filter for multiple repeats with bounded edit distanceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 in...
Source: Algorithms for Molecular Biology - January 30, 2009 Category: Molecular Biology Authors: Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira do Lago, Nadia Pisanti and Marie-France Sagot Source Type: journals

CHSMiner: a GUI tool to identify chromosomal homologous segmentsEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - January 15, 2009 Category: Molecular Biology Authors: Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu and Yixue Li Source Type: journals

Auto-validating von Neumann rejection sampling from small phylogenetic tree spacesEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - January 7, 2009 Category: Molecular Biology Authors: Raazesh Sainudiin and Thomas York Source Type: journals

HuMiTar: A sequence-based method for prediction of human microRNA targetsEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - December 22, 2008 Category: Molecular Biology Authors: Jishou Ruan, Hanzhe Chen, Lukasz Kurgan, Ke Chen, Chunsheng Kang and Peiyu Pu Source Type: journals

Syntenator: Multiple gene order alignments with a gene-specific scoring functionEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - November 6, 2008 Category: Molecular Biology Authors: Christian Rodelsperger and Christoph Dieterich Source Type: journals

Stability of Multiple Alignments and Phylogenetic Trees: An Analysis of ABC-Transporter ProteinsEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - November 6, 2008 Category: Molecular Biology Authors: Andreas WM Dress, Burkhard Morgenstern and Holger Wagner Source Type: journals

Fast Algorithms for Computing Sequence Distances by Exhaustive Substring CompositionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 inform...
Source: Algorithms for Molecular Biology - October 28, 2008 Category: Molecular Biology Authors: Alberto Apostolico and Olgert Denas Source Type: journals

"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measuresEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - August 29, 2008 Category: Molecular Biology Authors: Hans Binder, Knut Krohn and Stephan Preibisch Source Type: journals

"Hook"-calibration of GeneChip-microarrays: Theory and algorithmEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - August 29, 2008 Category: Molecular Biology Authors: Hans Binder and Stephan Preibisch Source Type: journals

A stitch in time: Efficient computation of genomic DNA melting bubblesEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - July 17, 2008 Category: Molecular Biology Authors: Eivind Tostesen Source Type: journals

A weighted average difference method for detecting differentially expressed genes from microarray dataEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - June 26, 2008 Category: Molecular Biology Authors: Koji Kadota, Yuji Nakai and Kentaro Shimizu Source Type: journals

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing mapsEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - June 26, 2008 Category: Molecular Biology Authors: Peter Meinicke, Thomas Lingner, Alexander Kaever, Kirstin Feussner, Cornelia Gobel, Ivo Feussner, Petr Karlovsky and Burkhard Morgenstern Source Type: journals

Noisy: identification of problematic columns in multiple sequence alignmentsEmail 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 - June 24, 2008 Category: Molecular Biology Authors: Andreas WM Dress, Christoph Flamm, Guido Fritzsch, Stefan Grunewald, Matthias Kruspe, Sonja J Prohaska and Peter F Stadler Source Type: journals

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignmentEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - May 27, 2008 Category: Molecular Biology Authors: Amarendran R Subramanian, Michael Kaufmann and Burkhard Morgenstern Source Type: journals

On the optimality of the neighbor-joining algorithmEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 equ...
Source: Algorithms for Molecular Biology - April 30, 2008 Category: Molecular Biology Authors: Kord Eickmeyer, Peter Huggins, Lior Pachter and Ruriko Yoshida Source Type: journals

Protein sequence and structure alignments within one frameworkEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - April 1, 2008 Category: Molecular Biology Authors: Gundolf Schenk, Thomas Margraf and Andrew E. Torda Source Type: journals

A scoring matrix approach to detecting miRNA target sitesEmail 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/ (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - March 31, 2008 Category: Molecular Biology Authors: Simon Moxon, Vincent Moulton and Jan T Kim Source Type: journals

Learning from positive examples when the negative class is undetermined- microRNA gene identificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - January 28, 2008 Category: Molecular Biology Authors: Malik Yousef, Segun Jung, Louise C Showe and Michael K Showe Source Type: journals

Reconstructing phylogenies from noisy quartets in polynomial time with a high success probabilityEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - January 24, 2008 Category: Molecular Biology Authors: Gang Wu, Ming-Yang Kao, Guohui Lin and Jia-Huai You Source Type: journals

Evaluating deterministic motif significance measures in protein databasesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - December 24, 2007 Category: Molecular Biology Authors: Pedro GABRIEL Ferreira and Paulo J. Azevedo Source Type: journals

Efficient and accurate P-value computation for Position Weight MatricesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - December 11, 2007 Category: Molecular Biology Authors: Helene Touzet and Jean-Stephane Varre Source Type: journals

Review of "Reconstructing Evolution: New mathematical and computational advances" edited by Olivier Gascuel and Mike SteelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
no abstract for this type of article (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - November 6, 2007 Category: Molecular Biology Authors: Andreas Spillner Source Type: journals

Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modulesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - October 10, 2007 Category: Molecular Biology Authors: Valentina Boeva, Julien Clement, Mireille Regnier, Mikhail A. Roytberg and Vsevolod J. Makeev Source Type: journals

Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - October 3, 2007 Category: Molecular Biology Authors: Rodrigo Gouveia-Oliveira and Anders G Pedersen Source Type: journals

Mapping sequences by partsEmail 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|.|t|.N) using O(|s|+|t|.N) memory space. Among all the numbers of parts tak...
Source: Algorithms for Molecular Biology - September 19, 2007 Category: Molecular Biology Authors: Gilles Didier and Carito Guziolowski Source Type: journals

A basic analysis toolkit for biological sequencesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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, ou...
Source: Algorithms for Molecular Biology - September 18, 2007 Category: Molecular Biology Authors: Raffaele Giancarlo, Alessandro Siragusa, Enrico Siragusa and Filippo Utro Source Type: journals

Local sequence alignments statistics: deviations from Gumbel statistics in the rare-event tailEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - July 11, 2007 Category: Molecular Biology Authors: Stefan Wolfsheimer, Bernd Burghardt and Alexander K Hartmann Source Type: journals

Consistency of the Neighbor-Net AlgorithmEmail 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 a f...
Source: Algorithms for Molecular Biology - June 28, 2007 Category: Molecular Biology Authors: David Bryant, Vincent Moulton and Andreas Spillner Source Type: journals

Characteristics of predictor sets found using differential prioritizationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - June 4, 2007 Category: Molecular Biology Authors: Chia Huey Ooi, Madhu Chetty and Shyh Wei Teng Source Type: journals

RNAstrand: reading direction of structured RNAs in multiple sequence alignmentsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - May 31, 2007 Category: Molecular Biology Authors: Kristin Reiche and Peter F Stadler Source Type: journals

GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP dataEmail 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. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - May 30, 2007 Category: Molecular Biology Authors: Koji Kadota, Ryoko Araki, Yuji Nakai and Masumi Abe 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.
This is a meeting report for the 6th SIGKDD Workshop on Data Mining in Bioinformatics. (Source: Algorithms for Molecular Biology)
Source: Algorithms for Molecular Biology - April 11, 2007 Category: Molecular Biology Authors: Mohammed J Zaki, George Karypis and Jiong Yang Source Type: journals

A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectoriesEmail 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 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 beco...
Source: Algorithms for Molecular Biology - April 4, 2007 Category: Molecular Biology Authors: Hui Yang, Srinivasan Parthasarathy and Duygu Ucar Source Type: journals

Transcriptional regulatory network discovery via multiple method integration: application to e.coli K12Email 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 that mor...
Source: Algorithms for Molecular Biology - March 30, 2007 Category: Molecular Biology Authors: Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Mike Trelinski and Peter Ortoleva Source Type: journals

PhyloScan: Identification of transcription factor binding sites using cross-species evidenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - January 23, 2007 Category: Molecular Biology Authors: C Steven Carmack, Lee Ann McCue, Lee A Newberg and Charles E Lawrence Source Type: journals

Probability-based model of protein-protein interactions on biological timescalesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - December 11, 2006 Category: Molecular Biology Authors: Alexander L Tournier, Paul W Fitzjohn and Paul A Bates Source Type: journals

A novel functional module detection algorithm for protein-protein interaction networkEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Algorithms for Molecular Biology - December 5, 2006 Category: Molecular Biology Authors: Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan Source Type: journals

A novel functional module detection algorithm for protein-protein interaction networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Algorithms for Molecular Biology - December 5, 2006 Category: Molecular Biology Authors: Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan Source Type: journals

Refining motifs by improving information content scores using neighborhood profile searchEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 Maxi...
Source: Algorithms for Molecular Biology - November 27, 2006 Category: Molecular Biology Authors: Chandan K Reddy, Yao-Chung Weng and Hsiao-Dong Chiang Source Type: journals