Evolutionary Bioinformatics Online最新文献_第8页

A Simple Derivation of the Distribution of Pairwise Local Protein Sequence Alignment Scores 两两局部蛋白质序列比对分数分布的简单推导

Evolutionary Bioinformatics Online Pub Date : 2008-01-01 DOI: 10.1177/117693430800400001

O. Bastien

{"title":"A Simple Derivation of the Distribution of Pairwise Local Protein Sequence Alignment Scores","authors":"O. Bastien","doi":"10.1177/117693430800400001","DOIUrl":"https://doi.org/10.1177/117693430800400001","url":null,"abstract":"Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. In the asymptotic limit of long sequences, the Karlin-Altschul model computes a P-value assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Using a simple approach combined with recent results in reliability theory, we demonstrate here that the Karlin-Altshul model can be derived with no reference to the extreme events theory. Sequences were considered as systems in which components are amino acids and having a high redundancy of Information reflected by their alignment scores. Evolution of the information shared between aligned components determined the Shared Amount of Information (SA.I.) between sequences, i.e. the score. The Gumbel distribution parameters of aligned sequences scores find here some theoretical rationale. The first is the Hazard Rate of the distribution of scores between residues and the second is the probability that two aligned residues do not lose bits of information (i.e. conserve an initial pairing score) when a mutation occurs.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133858797","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: 8

Examining Ancient Inter-domain Horizontal Gene Transfer 古代域间水平基因转移的研究

Evolutionary Bioinformatics Online Pub Date : 2008-01-01 DOI: 10.1177/117693430800400002

F. C. Almeida, M. Leszczyniecka, P. Fisher, R. DeSalle

{"title":"Examining Ancient Inter-domain Horizontal Gene Transfer","authors":"F. C. Almeida, M. Leszczyniecka, P. Fisher, R. DeSalle","doi":"10.1177/117693430800400002","DOIUrl":"https://doi.org/10.1177/117693430800400002","url":null,"abstract":"Details of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and analyze because of the extreme degree of divergence of genes in these three domains and because most evidence for such events are poorly supported. In addition, many researchers have suggested that the prevalence of IDHGT events early in the evolution of life would most likely obscure the patterns of divergence of major groups of organisms let alone allow the tracking of horizontal transfer at this level. In order to approach this problem, we mined the E. coli genome for genes with distinct paralogs. Using the 1,268 E. coli K-12 genes with 40% or higher similarity level to a paralog elsewhere in the E. coli genome we detected 95 genes found exclusively in Bacteria and Archaea and 86 genes found in Bacteria and Eukarya. These genes form the basis for our analysis of IDHGT. We also applied a newly developed statistical test (the node height test), to examine the robustness of these inferences and to corroborate the phylogenetically identified cases of ancient IDHGT. Our results suggest that ancient inter domain HGT is restricted to special cases, mostly involving symbiosis in eukaryotes and specific adaptations in prokaryotes. Only three genes in the Bacteria + Eukarya class (Deoxyxylulose-5-phosphate synthase (DXPS), fructose 1,6-phosphate aldolase class II protein and glucosamine-6-phosphate deaminase) and three genes–in the Bacteria + Archaea class (ABC-type FE3+ -siderophore transport system, ferrous iron transport protein B, and dipeptide transport protein) showed evidence of ancient IDHGT. However, we conclude that robust estimates of IDHGT will be very difficult to obtain due to the methodological limitations and the extreme sequence saturation of the genes suspected of being involved in IDHGT.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132940960","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: 15

The ABCs of MGR with DCJ 与DCJ一起了解MGR的基本知识

Evolutionary Bioinformatics Online Pub Date : 2008-01-01 DOI: 10.1177/117693430800400004

Zaky Adam, D. Sankoff

引用次数: 41

Why Should We Care About Molecular Coevolution? 为什么我们应该关心分子的共同进化?

Evolutionary Bioinformatics Online Pub Date : 2008-01-01 DOI: 10.1177/117693430800400003

F. Codoñer, M. Fares

引用次数: 74

Phylogenetic Study of the Evolution of PEP-Carboxykinase pep -羧基激酶进化的系统发育研究

Evolutionary Bioinformatics Online Pub Date : 2007-12-11 DOI: 10.4137/EBO.S288

S. Aich, L. Delbaere

引用次数: 23

Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians 122名白种人多位点SNP等位基因的相互作用与皮肤色素沉着变异

Evolutionary Bioinformatics Online Pub Date : 2007-09-06 DOI: 10.1177/117693430700300003

S. Anno, Takashi Abe, K. Sairyo, S. Kudo, Takushi Yamamoto, K. Ogata, V. Goel

{"title":"Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians","authors":"S. Anno, Takashi Abe, K. Sairyo, S. Kudo, Takushi Yamamoto, K. Ogata, V. Goel","doi":"10.1177/117693430700300003","DOIUrl":"https://doi.org/10.1177/117693430700300003","url":null,"abstract":"This study was undertaken to clarify the molecular basis for human skin color variation and the environmental adaptability to ultraviolet irradiation, with the ultimate goal of predicting the impact of changes in future environments on human health risk. One hundred twenty-two Caucasians living in Toledo, Ohio participated. Back and cheek skin were assayed for melanin as a quantitative trait marker. Buccal cell samples were collected and used for DNA extraction. DNA was used for SNP genotyping using the Masscode system, which entails two-step PCR amplification and a platform chemistry which allows cleavable mass spectrometry tags. The results show gene-gene interaction between SNP alleles at multiple loci (not necessarily on the same chromosome) contributes to inter-individual skin color variation while suggesting a high probability of linkage disequilibrium. Confirmation of these findings requires further study with other ethic groups to analyze the associations between SNP alleles at multiple loci and human skin color variation. Our overarching goal is to use remote sensing data to clarify the interaction between atmospheric environments and SNP allelic frequency and investigate human adaptability to ultraviolet irradiation. Such information should greatly assist in the prediction of the health effects of future environmental changes such as ozone depletion and increased ultraviolet exposure. If such health effects are to some extent predictable, it might be possible to prepare for such changes in advance and thus reduce the extent of their impact.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121331543","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: 4

Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions 基于蛋白质功能进化守恒的蛋白质-蛋白质相互作用预测

Evolutionary Bioinformatics Online Pub Date : 2007-08-08 DOI: 10.4137/EBO.S0

E. Kotelnikova, A. Kalinin, A. Yuryev, S. Maslov

{"title":"Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions","authors":"E. Kotelnikova, A. Kalinin, A. Yuryev, S. Maslov","doi":"10.4137/EBO.S0","DOIUrl":"https://doi.org/10.4137/EBO.S0","url":null,"abstract":"Motivation: Although a great deal of progress is being made in the development of fast and reliable experimental techniques to extract genome-wide networks of protein-protein and protein-DNA interactions, the sequencing of new genomes proceeds at an even faster rate. That is why there is a considerable need for reliable methods of in-silico prediction of protein interaction based solely on sequence similarity information and known interactions from well-studied organisms. This problem can be solved if a dependency exists between sequence similarity and the conservation of the proteins’ functions. Results: In this paper, we introduce a novel probabilistic method for prediction of protein-protein interactions using a new empirical probabilistic formula describing the loss of interactions between homologous proteins during the course of evolution. This formula describes an evolutional process quite similar to the process of the Earth’s population growth. In addition, our method favors predictions confirmed by several interacting pairs over predictions coming from a single interacting pair. Our approach is useful in working with “noisy” data such as those coming from high-throughput experiments. We have generated predictions for five “model” organisms: H. sapiens, D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae and evaluated the quality of these predictions.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"79 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114282168","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: 225

MapToGenome: A Comparative Genomic Tool that Aligns Transcript Maps to Sequenced Genomes MapToGenome:一个比较基因组工具，将转录图谱与测序基因组进行比对

Evolutionary Bioinformatics Online Pub Date : 2007-02-14 DOI: 10.1177/117693430700300023

S. Putta, J. Smith, C. Staben, S. Voss

{"title":"MapToGenome: A Comparative Genomic Tool that Aligns Transcript Maps to Sequenced Genomes","authors":"S. Putta, J. Smith, C. Staben, S. Voss","doi":"10.1177/117693430700300023","DOIUrl":"https://doi.org/10.1177/117693430700300023","url":null,"abstract":"Efforts to generate whole genome assemblies and dense genetic maps have provided a wealth of gene positional information for several vertebrate species. Comparing the relative location of orthologous genes among these genomes provides perspective on genome evolution and can aid in translating genetic information between distantly related organisms. However, large-scale comparisons between genetic maps and genome assemblies can prove challenging because genetic markers are commonly derived from transcribed sequences that are incompletely and variably annotated. We developed the program MapToGenome as a tool for comparing transcript maps and genome assemblies. MapToGenome processes sequence alignments between mapped transcripts and whole genome sequence while accounting for the presence of intronic sequences, and assigns orthology based on user-defined parameters. To illustrate the utility of this program, we used MapToGenome to process alignments between vertebrate genetic maps and genome assemblies 1) self/self alignments for maps and assemblies of the rat and zebrafish genome; 2) alignments between vertebrate transcript maps (rat, salamander, zebrafish, and medaka) and the chicken genome; and 3) alignments of the medaka and zebrafish maps to the pufferfish (Tetraodon nigroviridis) genome. Our results show that map-genome alignments can be improved by combining alignments across presumptive intron breaks and ignoring alignments for simple sequence length polymorphism (SSLP) marker sequences. Comparisons between vertebrate maps and genomes reveal broad patterns of conservation among vertebrate genomes and the differential effects of genome rearrangement over time and across lineages.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2007-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132181827","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: 4

Unravelling Selection Shifts Among Foot-and-Mouth Disease Virus (FMDV) Serotypes 揭示口蹄疫病毒(FMDV)血清型的选择转变

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200009

D. Tully, M. Fares

{"title":"Unravelling Selection Shifts Among Foot-and-Mouth Disease Virus (FMDV) Serotypes","authors":"D. Tully, M. Fares","doi":"10.1177/117693430600200009","DOIUrl":"https://doi.org/10.1177/117693430600200009","url":null,"abstract":"FMDV virus has been increasingly recognised as the most economically severe animal virus with a remarkable degree of antigenic diversity. Using an integrative evolutionary and computational approach we have compelling evidence for heterogeneity in the selection forces shaping the evolution of the seven different FMDV serotypes. Our results show that positive Darwinian selection has governed the evolution of the major antigenic regions of serotypes A, Asia1, O, SAT1 and SAT2, but not C or SAT3. Co-evolution between sites from antigenic regions under positive selection pinpoints their functional communication to generate immune-escape mutants while maintaining their ability to recognise the host-cell receptors. Neural network and functional divergence analyses strongly point to selection shifts between the different serotypes. Our results suggest that, unlike African FMDV serotypes, serotypes with wide geographical distribution have accumulated compensatory mutations as a strategy to ameliorate the effect of slightly deleterious mutations fixed by genetic drift. This strategy may have provided the virus by a flexibility to generate immune-escape mutants and yet recognise host-cell receptors. African serotypes presented no evidence for compensatory mutations. Our results support heterogeneous selective constraints affecting the different serotypes. This points to the possible accelerated rates of evolution diverging serotypes sharing geographical locations as to ameliorate the competition for the host.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"28 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":"125145923","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

Multiple Property Tolerance Analysis for the Evaluation of Missense Mutations 评价错义突变的多特性耐受性分析

Evolutionary Bioinformatics Online Pub Date : 2006-01-01 DOI: 10.1177/117693430600200019

Tai-Sung Lee, S. Potts, M. Mcginniss, C. Strom

{"title":"Multiple Property Tolerance Analysis for the Evaluation of Missense Mutations","authors":"Tai-Sung Lee, S. Potts, M. Mcginniss, C. Strom","doi":"10.1177/117693430600200019","DOIUrl":"https://doi.org/10.1177/117693430600200019","url":null,"abstract":"Computational prediction of the impact of a mutation on protein function is still not accurate enough for clinical diagnostics without additional human expert analysis. Sequence alignment-based methods have been extensively used but their results highly depend on the quality of the input alignments and the choice of sequences. Incorporating the structural information with alignments improves prediction accuracy. Here, we present a conservation of amino acid properties method for mutation prediction, Multiple Properties Tolerance Analysis (MuTA), and a new strategy, MuTA/S, to incorporate the solvent accessible surface (SAS) property into MuTA. Instead of combining multiple features by machine learning or mathematical methods, an intuitive strategy is used to divide the residues of a protein into different groups, and in each group the properties used is adjusted. The results for LacI, lysozyme, and HIV protease show that MuTA performs as well as the widely used SIFT algorithm while MuTA/S outperforms SIFT and MuTA by 2%–25% in terms of prediction accuracy. By incorporating the SAS term alone, the alignment dependency of overall prediction accuracy is significantly reduced. MuTA/S also defines a new way to incorporate any structural features and knowledge and may lead to more accurate predictions.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"50 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":"116282630","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: 1