OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes - PubMed (original) (raw)

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

Celine Scornavacca et al. Mol Biol Evol. 2019.

Abstract

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.

Keywords: coding sequences; comparative genomics; mammals; orthologous sequences; phylogenomics.

© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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Figures

Fig. 1.

Screenshots from the OrthoMaM website version 10. Here, the database is queried for CDSs with a relative evolutionary rate between 0.5 and 2, a GC3 between 23% and 45%, a parameter of the gamma distribution ranging from 1 to 2, and an alignment length >1,000 characters (top left). The result returns 126 target CDSs, for which information can be downloaded (bottom left). The longest CDS (ABCA13) is visualized with the corresponding phylogenetic information (top right) and AA alignment (bottom right).

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References

1. 1. Douzery EJP, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V.. 2014. OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals. Mol Biol Evol. 31(7):1923–1928. - PubMed
2. 1. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol. 7(10):e1002195.. - PMC - PubMed
3. 1. Katoh K, Standley DM.. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. - PMC - PubMed
4. 1. Philippe H, de Vienne DM, Ranwez V, Roure B, Baurain D, Delsuc F.. 2017. Pitfalls in supermatrix phylogenomics. Eur J Taxon. 283:1–25.
5. 1. Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, Douzery EJP.. 2007. OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. BMC Evol Biol. 7(1):241.. - PMC - PubMed

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