GECA: a fast tool for gene evolution and conservation analysis in eukaryotic protein families

Abstract

Abstract Summary: GECA is a fast, user-friendly and freely-available tool for representing gene exon/intron organization and highlighting changes in gene structure among members of a gene family. It relies on protein alignment, completed with the identification of common introns in the corresponding genes using CIWOG. GECA produces a main graphical representation showing the resulting aligned set of gene structures, where exons are to scale. The important and original feature of GECA is that it combines these gene structures with a symbolic display highlighting sequence similarity between subsequent genes. It is worth noting that this combination of gene structure with the indications of similarities between related genes allows rapid identification of possible events of gain or loss of introns, or points to erroneous structural annotations. The output image is generated in a portable network graphics format which can be used for scientific publications. Availability and implementation: Web-implemented version and source code are freely available at https://peroxibase.toulouse.inra.fr/geca_input_demo.php and a detailed example can be found at https://peroxibase.toulouse.inra.fr/geca_instructions.php Contact: mathe@lrsv.ups-tlse.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Keywords

Affiliated Institutions

• Centre National de la Recherche Scientifique FR
• Université Toulouse III - Paul Sabatier FR
• Laboratoire de Recherche en Sciences Végétales FR
• Université Fédérale de Toulouse Midi-Pyrénées FR

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