{"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/sopang-2-online-searching-over-a-pan-genome","title":"SOPanG 2: online searching over a pan-genome without false positives","arxiv_id":"2004.03033","date":"2020-04-06","proceeding":null,"authors":["Aleksander Cisłak","Szymon Grabowski"],"abstract":"Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any) match the entire query. Results: We augment the ED string with sources (individuals' indexes) and propose an extension of the SOPanG (Shift-Or for Pan-Genome) tool to report only true positive matches, omitting those not occurring in any of the haplotypes. The additional stage for checking the matches yields a penalty of less than 3.5% relative speed in practice, which means that SOPanG 2 is able to report pattern matches in a pan-genome, mapping them onto individuals, at the single-thread throughput of above 430 MB/s on real data. Availability and implementation: SOPanG 2 can be downloaded here: github.com/MrAlexSee/sopang","url_abs":"https://arxiv.org/abs/2004.03033v2","url_pdf":"https://arxiv.org/pdf/2004.03033v2.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":"links_only","authors_date_abstract":"arXiv metadata, CC0 1.0 (https://info.arxiv.org/help/license), from the Kaggle arXiv metadata snapshot of 2026-09-12"},"code_links":[{"paper_slug":"sopang-2-online-searching-over-a-pan-genome","repo_url":"https://github.com/MrAlexSee/sopang","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"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}