Large-scale assignment of orthology: back to phylogenetics?

被引：136

作者：

Gabaldon, Toni ^{[1
]}

机构：

[1] Ctr Genom Regulat, Bioinformat & Genom Program, Barcelona 08003, Spain

来源：

GENOME BIOLOGY | 2008年 / 9卷 / 10期

关键词：

D O I：

10.1186/gb-2008-9-10-235

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies.

引用

页数：6

共 36 条

[1] Optimal gene trees from sequences and species trees using a soft interpretation of parsimony [J].

Berglund-Sonnhammer, Ann-Charlotte ;

Steffansson, Par ;

Betts, Matthew J. ;

Liberles, David A. .

JOURNAL OF MOLECULAR EVOLUTION, 2006, 63 (02) :240-250

[2] NOTUNG: A program for dating gene duplications and optimizing gene family trees [J].

Chen, K ;

Durand, D ;

Farach-Colton, M .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2000, 7 (3-4) :429-447

[3] OrthologID: automation of genome-scale ortholog identification within a parsimony framework [J].

Chiu, JC ;

Lee, EK ;

Egan, MG ;

Sarkar, IN ;

Coruzzi, GM ;

DeSalle, R .

BIOINFORMATICS, 2006, 22 (06) :699-707

[4] A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database [J].

Dehal, Paramvir S. ;

Boore, Jeffrey L. .

BMC BIOINFORMATICS, 2006, 7 (1)

[5] THE MULTIPLICITY OF DOMAINS IN PROTEINS [J].

DOOLITTLE, RF .

ANNUAL REVIEW OF BIOCHEMISTRY, 1995, 64 :287-314

[6] Tree pattern matching in phylogenetic trees:: automatic search for orthologs or paralogs in homologous gene sequence databases [J].

Dufayard, JF ;

Duret, L ;

Penel, S ;

Gouy, M ;

Rechenmann, F ;

Perrière, G .

BIOINFORMATICS, 2005, 21 (11) :2596-2603

[7] A hybrid micro-macroevolutionary approach to gene tree reconstruction [J].

Durand, D ;

Halldórsson, BV ;

Vernot, B .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2006, 13 (02) :320-335

[8] Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis [J].

Eisen, JA .

GENOME RESEARCH, 1998, 8 (03) :163-167

[9] DISTINGUISHING HOMOLOGOUS FROM ANALOGOUS PROTEINS [J].

FITCH, WM .

SYSTEMATIC ZOOLOGY, 1970, 19 (02) :99-&

[10] Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes [J].

Gabaldón, T ;

Huynen, MA .

BIOINFORMATICS, 2005, 21 :144-150

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