Enhanced automated function prediction using distantly related sequences and contextual association by PFP.

TitleEnhanced automated function prediction using distantly related sequences and contextual association by PFP.
Publication TypeJournal Article
Year of Publication2006
AuthorsHawkins T, Luban S, Kihara D
JournalProtein Sci
Volume15
Issue6
Pagination1550-6
Date Published2006 Jun
ISSN0961-8368
KeywordsAlgorithms, Computational Biology, Databases, Protein, Proteins
Abstract

The impetus for the recent development and emergence of automated function prediction methods is an exponentially growing flood of new experimental data, the interpretation of which is hindered by a shortage of reliable annotations for proteins that lack experimental characterization or significant homologs in current databases. Here we introduce PFP, an automated function prediction server that provides the most probable annotations for a query sequence in each of the three branches of the Gene Ontology: biological process, molecular function, and cellular component. Rather than utilizing precise pattern matching to identify functional motifs in the sequences and structures of these proteins, we designed PFP to increase the coverage of function annotation by lowering resolution of predictions when a detailed function is not predictable. To do this we extend a traditional PSI-BLAST search by extracting and scoring annotations (GO terms) individually, including annotations from distantly related sequences, and applying a novel data mining tool, the Function Association Matrix, to score strongly associated pairs of annotations. We show that PFP can correctly assign function using only weakly similar sequences with a significantly better accuracy and coverage than a standard PSI-BLAST search, improving it more than fivefold. The most descriptive annotations predicted by PFP (GO depth > or = 8) can identify a significant subgraph in the GO with > 60% accuracy and approximately 100% coverage for our benchmark set. We also provide examples of the superb performance of PFP in an assessment of automated function prediction servers at the Automated Function Prediction Special Interest Group meeting at ISMB 2005 (AFP-SIG '05).

DOI10.1110/ps.062153506
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/16672240?dopt=Abstract
PMCPMC2242549
Alternate TitleProtein Sci.
PubMed ID16672240