Big data and other challenges in the quest for orthologs.

Détails

Ressource 1Télécharger: BIB_172DE4708266.P001.pdf (202.15 [Ko])
Etat: Serval
Version: de l'auteur
ID Serval
serval:BIB_172DE4708266
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Synthèse (review): revue aussi complète que possible des connaissances sur un sujet, rédigée à partir de l'analyse exhaustive des travaux publiés.
Collection
Publications
Titre
Big data and other challenges in the quest for orthologs.
Périodique
Bioinformatics
Auteur(s)
Sonnhammer E.L., Gabaldón T., Sousa da Silva A.W., Martin M., Robinson-Rechavi M., Boeckmann B., Thomas P.D., Dessimoz C.
Collaborateur(s)
Quest for Orthologs consortium
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Statut éditorial
Publié
Date de publication
2014
Peer-reviewed
Oui
Volume
30
Numéro
21
Pages
2993-2998
Langue
anglais
Résumé
Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking.
AVAILABILITY AND IMPLEMENTATION: All such materials are available at http://questfororthologs.org.
CONTACT: erik.sonnhammer@scilifelab.se or c.dessimoz@ucl.ac.uk.
Pubmed
Web of science
Création de la notice
17/07/2014 8:48
Dernière modification de la notice
03/03/2018 14:17
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