title: An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates.
abstract: Variable (V) domains of immunoglobulins (Ig) and T cell receptors (TCR) are generated from genomic V gene segments (V-genes). At present, such V-genes have been annotated only within the genome of a few species. We have developed a bioinformatics tool that accelerates the task of identifying functional V-genes from genome datasets. Automated recognition is accomplished by recognizing key V-gene signatures, such as recombination signal sequences, size of the exon region, and position of amino acid motifs within the translated exon. This algorithm also classifies extracted V-genes into either TCR or Ig loci. We describe the implementation of the algorithm and validate its accuracy by comparing V-genes identified from the human and mouse genomes with known V-gene annotations documented and available in public repositories. The advantages and utility of the algorithm are illustrated by using it to identify functional V-genes in the rat genome, where V-gene annotation is still incomplete. This allowed us to perform a comparative human-rodent phylogenetic analysis based on V-genes that supports the hypothesis that distinct evolutionary pressures shape the TCRs and Igs V-gene repertoires. Our program, together with a user graphical interface, is available as open-source software, downloadable at http://code.google.com/p/vgenextract/.
authors.affiliation: School of Computer Engineering, University of Vigo, 32004 Ourense, Spain. dnolivieri@gmail.com
authors.forename: David
authors.initials: D
authors.lastname: Olivieri
authors.forename: Jose
authors.initials: J
authors.lastname: Faro
authors.forename: Bernardo
authors.initials: B
authors.lastname: von Haeften
authors.forename: Christian
authors.initials: C
authors.lastname: Sánchez-Espinel
authors.forename: Francisco
authors.initials: F
authors.lastname: Gambón-Deza
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D005803:Genes, Immunoglobulin; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D007135:Immunoglobulin Variable Region / Q000235:genetics*; D051379:Mice; D010802:Phylogeny; D051381:Rats; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D012984:Software
chemical_list: D007135:Immunoglobulin Variable Region; D011948:Receptors, Antigen, T-Cell