{"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/mafcounter-an-efficient-tool-for-counting-the","title":"MAFcounter: An efficient tool for counting the occurrences of k-mers in MAF files","arxiv_id":"2411.19427","date":"2024-11-29","proceeding":null,"authors":["Michail Patsakis","Kimonas Provatas","Ioannis Mouratidis","Ilias Georgakopoulos-Soares"],"abstract":"Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity patterns, providing valuable insights into sequence conservation, evolutionary relationships and for functional analyses. Typically, sequence alignments are stored in formats such as the Multiple Alignment Format (MAF). Counting k-mer occurrences is a crucial task in many computational biology applications, but currently, there is no algorithm designed for k-mer counting in alignment files. Results: We have developed MAFcounter, the first k-mer counter dedicated to alignment files. MAFcounter is multithreaded, fast, and memory efficient, enabling k-mer counting in DNA and protein sequence alignment files. Availability: The MAFcounter package and its Python bindings are released under GPL license as a multi-platform application and are available at: https://github.com/Georgakopoulos-Soares-lab/MAFcounter","url_abs":"https://arxiv.org/abs/2411.19427v1","url_pdf":"https://arxiv.org/pdf/2411.19427v1.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":"mafcounter-an-efficient-tool-for-counting-the","repo_url":"https://github.com/georgakopoulos-soares-lab/mafcounter","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}