Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

Tópicos

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Resumo

The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods.

Resumo Limpo

goal gene ontolog go project provid uniform way describ function gene product organ across kingdom life therebi enabl analysi genom data protein annot either base experi predict protein sequenc sinc sequenc experiment character avail annot need base predict make accur infer possibl go consortium refer genom project use explicit evolutionari framework infer annot protein broad set genom experiment annot semiautom manner compon pipelin select sequenc build multipl sequenc align phylogenet tree retriev experiment annot deposit infer annot fulli autom howev crucial step pipelin reli softwareassist curat expert biologist curat tool phylogenet annot infer tool paint help curat infer annot among member protein famili paint allow curat make precis assert function gain lost evolut record evid eg experiment support go annot phylogenet inform includ ortholog assert articl describ use paint infer protein function phylogenet context emphasi strength limit guidelin also discuss specif exampl show paint annot compar generat high use homologybas method

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