Decombinator is a tool for the fast, efficient analysis of T cell receptor (TcR) repertoire samples, designed to be accessible to those with no previous programming experience. It is based on the Aho-Corasick algorithm which uses a finite state automaton (FSA) to quickly assign a specific V and J gene segment. From these assignments, it is then able to determine the number of germline V and J deletions and the string of contiguous nucleotides which lie between the 3′ end of the V gene segment and the 5′ end of the J gene segment. These 5 variables form the identier which uniquely categorises each distinct TcR sequence.
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Bioinformatics. 2013 Mar 1;29(5):542-50. doi: 10.1093/bioinformatics/btt004. Epub 2013 Jan 9.
Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine.
Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B.