Big data and other challenges in the quest for orthologs.

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Ressource 1Download: BIB_172DE4708266.P001.pdf (202.15 [Ko])
State: Public
Version: author
Serval ID
serval:BIB_172DE4708266
Type
Article: article from journal or magazin.
Publication sub-type
Review (review): journal as complete as possible of one specific subject, written based on exhaustive analyses from published work.
Collection
Publications
Institution
Title
Big data and other challenges in the quest for orthologs.
Journal
Bioinformatics
Author(s)
Sonnhammer E.L., Gabaldón T., Sousa da Silva A.W., Martin M., Robinson-Rechavi M., Boeckmann B., Thomas P.D., Dessimoz C.
Working group(s)
Quest for Orthologs consortium
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Publication state
Published
Issued date
2014
Peer-reviewed
Oui
Volume
30
Number
21
Pages
2993-2998
Language
english
Abstract
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
Open Access
Yes
Create date
17/07/2014 7:48
Last modification date
03/01/2020 19:19
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