IsoSel: Protein Isoform Selector for phylogenetic reconstructions

PLoS One. 2017 Mar 21;12(3):e0174250. doi: 10.1371/journal.pone.0174250. eCollection 2017.

Abstract

The reliability of molecular phylogenies is strongly dependent on the quality of the assembled datasets. In the case of eukaryotes, the selection of only one protein isoform per genomic locus is mandatory to avoid biases linked to redundancy. Here, we present IsoSel, a tool devoted to the selection of alternative isoforms in the context of phylogenetic reconstruction. It provides a better alternative to the widely used approach consisting in the selection of the longest isoforms and it performs better than Guidance, its only available counterpart. IsoSel is publicly available at http://doua.prabi.fr/software/isosel.

MeSH terms

  • Algorithms*
  • Alternative Splicing / genetics
  • Amino Acid Sequence / genetics
  • Animals
  • Base Sequence
  • Computational Biology / methods*
  • Humans
  • Phylogeny
  • Plants / genetics
  • Protein Isoforms / genetics*
  • Sequence Analysis, DNA / methods*
  • Software*

Substances

  • Protein Isoforms

Grant support

This work was supported by grants from the CNRS, the Institut Français de Bioinformatique to GP, the France Génomique consortium for GP, and the Région Rhône-Alpes PhD thesis grant 13-012735-01, which was funding the Ph.D of HP. CBA is a member of the Institut Universitaire de France and is funded by the “Ancestrome” project through the Agence Nationale de la Recherche grant ANR-10-BINF-01-01. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.