IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis

• DOI: 10.1093/bioinformatics/btv238
• Publication Date: 2015-06-13T17:12:36Z
• Authors: Yana Safonova; Stefano Bonissone; Eugene Kurpilyansky; Ekaterina Starostina; Alla Lapidus; Jeremy Stinson; Laura DePalatis; Wendy Sandoval; Jennie Lill; Pavel A. Pevzner
• Keywords: Python; Antibody Repertoire

Abstract The analysis of concentrations circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem immunoinformatics. two current approaches to the antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since are not directly encoded germline but extensively diversified by somatic recombination hypermutations. Therefore, protein database required for interpretation spectra from custom each individual. Although such can be constructed via NGS, reads generated NGS error-prone even single nucleotide error precludes identification peptide standard proteomics tools. Here, we IgRepertoireConstructor algorithm that performs error-correction immunosequencing uses validate repertoires. Availability implementation: open source freely available as C++ Python program running on all Unix-compatible platforms. code http://bioinf.spbau.ru/igtools. Contact: [e-mail] Supplementary information: data at Bioinformatics online.