Evolutionary Bioinformatics Online最新文献_第9页

MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution MBEToolbox 2.0:用于分子生物学和进化的MATLAB工具箱的增强版本

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200002

James J. Cai, D. Smith, X. Xia, K. Yuen

引用次数: 10

Improved Heuristics for Minimum-Flip Supertree Construction 最小翻转超树构造的改进启发式算法

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200003

Duhong Chen, O. Eulenstein, David Fernández-Baca, J. G. Burleigh

引用次数: 41

Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction 基于模式的系统发育距离估计与树重建

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200016

M. Höhl, I. Rigoutsos, M. Ragan

{"title":"Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction","authors":"M. Höhl, I. Rigoutsos, M. Ragan","doi":"10.1177/117693430600200016","DOIUrl":"https://doi.org/10.1177/117693430600200016","url":null,"abstract":"We have developed an alignment-free method that calculates phylogenetic distances using a maximum-likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au), we have created a data set of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131899130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 49

A Fast and Specific Alignment Method for Minisatellite Maps 一种小卫星地图快速特异对准方法

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200025

S. Bérard, F. Nicolas, J. Buard, O. Gascuel, Eric Rivals

{"title":"A Fast and Specific Alignment Method for Minisatellite Maps","authors":"S. Bérard, F. Nicolas, J. Buard, O. Gascuel, Eric Rivals","doi":"10.1177/117693430600200025","DOIUrl":"https://doi.org/10.1177/117693430600200025","url":null,"abstract":"Background Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects neutrally evolving regions, the polymorphism in length (i.e., in number of copies) of minisatellites proved useful in population genetics. Motivation In these tandem repeat sequences, different mutational mechanisms let the number of copies, as well as the copies themselves, vary. Especially, the interspersion of events of tandem duplication/contraction and of punctual mutation makes the succession of variant repeats much more informative than the sole allele length. To exploit this information requires the ability to align minisatellite alleles by accounting for both punctual mutations and tandem duplications. Results We propose a minisatellite maps alignment program that improves on previous solutions. Our new program is faster, simpler, considers an extended evolutionary model, and is available to the community. We test it on the data set of 609 alleles of the MSY1 (DYF155S1) human minisatellite and confirm its ability to recover known evolutionary signals. Our experiments highlight that the informativeness of minisatellites resides in their length and composition polymorphisms. Exploiting both simultaneously is critical to unravel the implications of variable minisatellites in the control of gene expression and diseases. Availability Software is available at http://atgc.lirmm.fr/ms_align/","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"47 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125759183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 17

Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny 估计在一个给定的系统发育中物种形成或合并事件的相对顺序

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200012

Tanja Gernhard, Daniel J. Ford, R. Vos, M. Steel

引用次数: 9

A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences 用606个序列的极大似然、分裂图和基序分析推断槭核核糖体DNA系统发育

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200014

G. Grimm, S. Renner, A. Stamatakis, V. Hemleben

{"title":"A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences","authors":"G. Grimm, S. Renner, A. Stamatakis, V. Hemleben","doi":"10.1177/117693430600200014","DOIUrl":"https://doi.org/10.1177/117693430600200014","url":null,"abstract":"The multi-copy internal transcribed spacer (ITS) region of nuclear ribosomal DNA is widely used to infer phylogenetic relationships among closely related taxa. Here we use maximum likelihood (ML) and splits graph analyses to extract phylogenetic information from ~ 600 mostly cloned ITS sequences, representing 81 species and subspecies of Acer, and both species of its sister Dipteronia. Additional analyses compared sequence motifs in Acer and several hundred Ana-cardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae ITS sequences in GenBank. We also assessed the effects of using smaller data sets of consensus sequences with ambiguity coding (accounting for within-species variation) instead of the full (partly redundant) original sequences. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks largely agree with morphology-based classifications; of de Jong's (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Most nodes had higher bootstrap support with matrices of 105 or 40 consensus sequences than with the original matrix. Within-taxon ITS divergence did not differ between diploid and polyploid Acer, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"108 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134403488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 89

Co-evolutionary Rates of Functionally Related Yeast Genes 功能相关酵母基因的共同进化速率

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200017

L. Mariño-Ramírez, O. Bodenreider, N. Kantz, I. Jordan

{"title":"Co-evolutionary Rates of Functionally Related Yeast Genes","authors":"L. Mariño-Ramírez, O. Bodenreider, N. Kantz, I. Jordan","doi":"10.1177/117693430600200017","DOIUrl":"https://doi.org/10.1177/117693430600200017","url":null,"abstract":"Evolutionary knowledge is often used to facilitate computational attempts at gene function prediction. One rich source of evolutionary information is the relative rates of gene sequence divergence, and in this report we explore the connection between gene evolutionary rates and function. We performed a genome-scale evaluation of the relationship between evolutionary rates and functional annotations for the yeast Saccharomyces cerevisiae. Non-synonymous (dN) and synonymous (dS) substitution rates were calculated for 1,095 orthologous gene sets common to S. cerevisiae and six other closely related yeast species. Differences in evolutionary rates between pairs of genes (ΔdN & ΔdS) were then compared to their functional similarities (sGO), which were measured using Gene Ontology (GO) annotations. Substantial and statistically significant correlations were found between ΔdN and sGO, whereas there is no apparent relationship between ΔdS and sGO. These results are consistent with a mode of action for natural selection that is based on similar rates of elimination of deleterious protein coding sequence variants for functionally related genes. The connection between gene evolutionary rates and function was stronger than seen for phylogenetic profiles, which have previously been employed to inform functional inference. The co-evolution of functionally related yeast genes points to the relevance of specific function for the efficacy of natural selection and underscores the utility of gene evolutionary rates for functional predictions.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114268636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 24

Positional Homology in Bacterial Genomes 细菌基因组的位置同源性

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200031

I. Burgetz, Salimah Shariff, A. Pang, E. Tillier

{"title":"Positional Homology in Bacterial Genomes","authors":"I. Burgetz, Salimah Shariff, A. Pang, E. Tillier","doi":"10.1177/117693430600200031","DOIUrl":"https://doi.org/10.1177/117693430600200031","url":null,"abstract":"In comparative genomic studies, syntenic groups of homologous sequence in the same order have been used as supplementary information that can be used in helping to determine the orthology of the compared sequences. The assumption is that orthologous gene copies are more likely to share the same genome positions and share the same gene neighbors. In this study we have defined positional homologs as those that also have homologous neighboring genes and we investigated the usefulness of this distinction for bacterial comparative genomics. We considered the identification of positionaly homologous gene pairs in bacterial genomes using protein and DNA sequence level alignments and found that the positional homologs had on average relatively lower rates of substitution at the DNA level (synonymous substitutions) than duplicate homologs in different genomic locations, regardless of the level of protein sequence divergence (measured with non-synonymous substitution rate). Since gene order conservation can indicate accuracy of orthology assignments, we also considered the effect of imposing certain alignment quality requirements on the sensitivity and specificity of identification of protein pairs by BLAST and FASTA when neighboring information is not available and in comparisons where gene order is not conserved. We found that the addition of a stringency filter based on the second best hits was an efficient way to remove dubious ortholog identifications in BLAST and FASTA analyses. Gene order conservation and DNA sequence homology are useful to consider in comparative genomic studies as they may indicate different orthology assignments than protein sequence homology alone.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121258787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19

CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies CoMET:用于比较系统发育上连续性状进化模型的Mesquite软件包

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200022

Chunghau Lee, S. Blay, A. Mooers, Ambuj K. Singh, Todd H. Oakley

引用次数: 37

Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes HIV-1包膜基因祖先序列重建的变异来源

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200027

H. Ross, D. Nickle, Yi Liu, Laura Heath, M. Jensen, A. Rodrigo, J. Mullins

{"title":"Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes","authors":"H. Ross, D. Nickle, Yi Liu, Laura Heath, M. Jensen, A. Rodrigo, J. Mullins","doi":"10.1177/117693430600200027","DOIUrl":"https://doi.org/10.1177/117693430600200027","url":null,"abstract":"We characterized the variation in the reconstructed ancestor of 118 HIV-1 envelope gene sequences arising from the methods used for (a) estimating and (b) rooting the phylogenetic tree, and (c) reconstructing the ancestor on that tree, from (d) the sequence format, and from (e) the number of input sequences. The method of rooting the tree was responsible for most of the sequence variation both among the reconstructed ancestral sequences and between the ancestral and observed sequences. Variation in predicted 3-D structural properties of the ancestors mirrored their sequence variation. The observed sequence consensus and ancestral sequences from center-rooted trees were most similar in all predicted attributes. Only for the predicted number of N-glycosylation sites was there a difference between MP and ML methods of reconstruction. Taxon sampling effects were observed only for outgroup-rooted trees, not center-rooted, reflecting the occurrence of several divergent basal sequences. Thus, for sequences exhibiting a radial phylogenetic tree, as does HIV-1, most of the variation in the estimated ancestor arises from the method of rooting the phylogenetic tree. Those investigating the ancestors of genes exhibiting such a radial tree should pay particular attention to alternate rooting methods in order to obtain a representative sample of ancestors.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125097197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9