Interpreting Gene Ontology Annotations Derived from Sequence Homology Methods.
Gain of function
Gene ontology
Homology annotation
Loss of function
Phylogenetic annotation
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2024
2024
Historique:
medline:
12
7
2024
pubmed:
12
7
2024
entrez:
12
7
2024
Statut:
ppublish
Résumé
The Gene Ontology (GO) project describes the functions of the gene products of organisms from all kingdoms of life in a standardized way, enabling powerful analyses of experiments involving genome-wide analysis. The scientific literature is used to convert experimental results into GO annotations that systematically classify gene products' functions. However, to address the fact that only a minor fraction of all genes has been characterized experimentally, multiple predictive methods to assign GO annotations have been developed since the inception of GO. Sequence homologies between novel genes and genes with known functions help to approximate the roles of these non-characterized genes. Here we describe the main sequence homology methods to produce annotations: pairwise comparison (BLAST), protein profile models (InterPro), and phylogenetic-based annotation (PAINT). Some of these methods can be implemented with genome analysis pipelines (BLAST and InterPro2GO), while PAINT is curated by the GO consortium.
Identifiants
pubmed: 38995546
doi: 10.1007/978-1-0716-4007-4_15
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
285-298Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
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