The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

Afrasiabi, Cyrus; Samad, Bushra; Dineen, David; Meacham, Christopher; Sjölander, Kimmen

doi:10.1093/nar/gkt399

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

Journal Article · Sat May 18 00:00:00 EDT 2013 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkt399· OSTI ID:1904526

Afrasiabi, Cyrus ^[1]; Samad, Bushra ^[2]; Dineen, David ^[3]; Meacham, Christopher ^[3]; Sjölander, Kimmen ^[3]

University of California, Berkeley, CA (United States). QB3 Institute; Univ. of California, Berkeley, CA
University of California, Berkeley, CA (United States)
University of California, Berkeley, CA (United States). QB3 Institute

The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases.

View Accepted Manuscript (DOE)

Research Organization:: University of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0004916

OSTI ID:: 1904526

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: W1 Vol. 41; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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The OMA orthology database in 2015: Function predictions, better plant support, synteny view and other improvements Altenhoff, Adrian Michael; Škunca, Nives; Glover, Natasha ETH Zurich https://doi.org/10.3929/ethz-b-000106322	text	January 2015

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