{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/consistency-of-vdj-rearrangement-and","title":"Consistency of VDJ rearrangement and substitution parameters enables accurate B cell receptor sequence annotation","arxiv_id":"1503.04224","date":"2015-05-28","proceeding":null,"authors":[],"abstract":"VDJ rearrangement and somatic hypermutation work together to produce\nantibody-coding B cell receptor (BCR) sequences for a remarkable diversity of\nantigens. It is now possible to sequence these BCRs in high throughput;\nanalysis of these sequences is bringing new insight into how antibodies\ndevelop, in particular for broadly-neutralizing antibodies against HIV and\ninfluenza. A fundamental step in such sequence analysis is to annotate each\nbase as coming from a specific one of the V, D, or J genes, or from an\nN-addition (a.k.a. non-templated insertion). Previous work has used simple\nparametric distributions to model transitions from state to state in a hidden\nMarkov model (HMM) of VDJ recombination, and assumed that mutations occur via\nthe same process across sites. However, codon frame and other effects have been\nobserved to violate these parametric assumptions for such coding sequences,\nsuggesting that a non-parametric approach to modeling the recombination process\ncould be useful. In our paper, we find that indeed large modern data sets\nsuggest a model using parameter-rich per-allele categorical distributions for\nHMM transition probabilities and per-allele-per-position mutation\nprobabilities, and that using such a model for inference leads to significantly\nimproved results. We present an accurate and efficient BCR sequence annotation\nsoftware package using a novel HMM \"factorization\" strategy. This package,\ncalled partis (https://github.com/psathyrella/partis/), is built on a new\ngeneral-purpose HMM compiler that can perform efficient inference given a\nsimple text description of an HMM.","url_abs":"http://arxiv.org/abs/1503.04224v2","url_pdf":"http://arxiv.org/pdf/1503.04224v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"consistency-of-vdj-rearrangement-and","repo_url":"https://github.com/psathyrella/partis","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}