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Mol Biol Evol. 2014 Jul;31(7):1923-8. doi: 10.1093/molbev/msu132. Epub 2014 Apr 9.

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals.

Author information

1
Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS IRD, Université Montpellier 2, Montpellier, France emmanuel.douzery@univ-montp2.fr.
2
Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS IRD, Université Montpellier 2, Montpellier, France.
3
Montpellier SupAgro, UMR AGAP, Montpellier, France.

Abstract

Comparative genomic studies extensively rely on alignments of orthologous sequences. Yet, selecting, gathering, and aligning orthologous exons and protein-coding sequences (CDS) that are relevant for a given evolutionary analysis can be a difficult and time-consuming task. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework. Since its first release in 2007, OrthoMaM has regularly evolved, not only to include newly available genomes but also to incorporate up-to-date software in its analytic pipeline. This eighth release integrates the 40 complete mammalian genomes available in Ensembl v73 and provides alignments, phylogenies, evolutionary descriptor information, and functional annotations for 13,404 single-copy orthologous CDS and 6,953 long exons. The graphical interface allows to easily explore OrthoMaM to identify markers with specific characteristics (e.g., taxa availability, alignment size, %G+C, evolutionary rate, chromosome location). It hence provides an efficient solution to sample preprocessed markers adapted to user-specific needs. OrthoMaM has proven to be a valuable resource for researchers interested in mammalian phylogenomics, evolutionary genomics, and has served as a source of benchmark empirical data sets in several methodological studies. OrthoMaM is available for browsing, query and complete or filtered downloads at http://www.orthomam.univ-montp2.fr/.

KEYWORDS:

coding sequences; comparative genomics; mammals; orthologous sequences; phylogenomics

PMID:
24723423
DOI:
10.1093/molbev/msu132
[Indexed for MEDLINE]

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