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Bioinformatics. 2012 May 15;28(10):1398-9. doi: 10.1093/bioinformatics/bts153. Epub 2012 Mar 29.

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

Author information

1
Université de Toulouse, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617 Auze ville, F-31326 Castanet-Tolosan, France.

Abstract

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.

PMID:
22467908
DOI:
10.1093/bioinformatics/bts153
[Indexed for MEDLINE]

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