ArticleImmunogenetics2013
An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates.
Article in Immunogenetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- ALIGaToR: A tool for the automated annotation of immunoglobulin and T cell receptor genomic loci.bioRxiv : the preprint server for biology · 2025Article
- Development of ferret immune repertoire reference resources and single-cell-based high-throughput profiling assays.Journal of virology · 2025Article
- Unique TCR loci architecture in newts: TRA and TRD separation inFrontiers in immunology · 2025Article
- ALIGaToR: a tool for the automated annotation of immunoglobulin and T cell receptor genomic loci.Oxford open immunology · 2025Article
- Unraveling the chicken T cell repertoire with enhanced genome annotation.Frontiers in immunology · 2024Article
- Gene prediction in the immunoglobulin loci.Genome research · 2022Article
- Distinct disease features in chimpanzees infected with a precore HBV mutant associated with acute liver failure in humans.PLoS pathogens · 2020Article
- Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm.Computational and mathematical methods in medicine · 2019Article
- Profiling of the TCRβ repertoire in non-model species using high-throughput sequencing.Scientific reports · 2018Article
- Comprehensive annotation and evolutionary insights into the canine (Canis lupus familiaris) antigen receptor loci.Immunogenetics · 2018Article
- Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads.PLoS computational biology · 2016Article
- Evolution of V genes from the TRV loci of mammals.Immunogenetics · 2015Article
- V genes in primates from whole genome sequencing data.Immunogenetics · 2015Article
- Genomic V exons from whole genome shotgun data in reptiles.Immunogenetics · 2014Article
- Expressed IgH μ and τ transcripts share diversity segment in ranched Thunnus orientalis.Developmental and comparative immunology · 2014Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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/.
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