ArticleNucleic acids research2013
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 24 citations in OpenAlex.
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- HIPPI: highly accurate protein family classification with ensembles of HMMs.BMC genomics · 2016Article
- A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.BMC bioinformatics · 2016Article
- Diversity in protein domain superfamilies.Current opinion in genetics & development · 2015Review
- The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.Nucleic acids research · 2015Article
- A RESTful API for accessing microbial community data for MG-RAST.PLoS computational biology · 2015Article
- FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.Nucleic acids research · 2014Article
- morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring.BMC bioinformatics · 2014Article
- PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.Nucleic acids research · 2014Article
- Quickly finding orthologs as reciprocal best hits with BLAT, LAST, and UBLAST: how much do we miss?PloS one · 2014Article
- An introduction to the analysis of shotgun metagenomic data.Frontiers in plant science · 2014Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.
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