OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes

Celine Scornavacca (1) , Khalid Belkhir (1) , Jimmy Lopez (1) , Rémy Dernat (1) , Frédéric Delsuc (1) , Emmanuel J.P. Douzery (1) , Vincent Ranwez (2)

1 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
2 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales

We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high-quality computed with state-of-the-art methods on up-to-date data. The main contribution of this version is the increase in the number of taxa: 116 mammalian genomes for 14,509 one-to-one orthologous genes. This has been made possible by the combination of genomic data deposited in Ensembl complemented by additional good-quality genomes only available in NCBI. Version 10 users will benefit from pipeline improvements and a completely redesigned web-interface.

Mots clés: mammals; orthologous sequences; comparative genomics; phylogenomics; coding sequences

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]; Génétique des populations [q-bio.PE]; Génomique, Transcriptomique et Protéomique [q-bio.GN]; Biodiversité et Ecologie

Celine Scornavacca, Khalid Belkhir, Jimmy Lopez, Rémy Dernat, Frédéric Delsuc, et al.. OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes. Molecular Biology and Evolution, 2019, 36 (4), pp.861-862. ⟨10.1093/molbev/msz015⟩. ⟨hal-02139915⟩