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PMID: 16381935 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

TreeFam: a curated database of phylogenetic trees of animal gene families.

Nucleic acids research ·Vol. 34 ·No. Database issue ·2006-01-01 ·Pages D572-80

Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R

Abstract

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; approximately 40-85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at http://www.treefam.org and http://treefam.genomics.org.cn.

MeSH Terms
Animals Databases, Genetic Evolution, Molecular Genes Genomics Humans Internet Mice Phylogeny Proteins/classification,genetics Rats Software User-Computer Interface
Chemicals
Proteins
Authors & Affiliations
15 authors, click to expand affiliations / ORCID
Li Heng
Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China.
Coghlan Avril
Ruan Jue
Coin Lachlan James
Hériché Jean-Karim
Osmotherly Lara
Li Ruiqiang
Liu Tao
Zhang Zhang
Bolund Lars
Wong Gane Ka-Shu
Zheng Weimou
Dehal Paramvir
Wang Jun
Durbin Richard
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkj118
Published
2006-01-01
Pages
D572-80
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1347480
Subset
IM
Grants
Wellcome Trust · United Kingdom
External Links
PubMed source DOI: 10.1093/nar/gkj118 PMC Full Text View journal details
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