{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T05:35:33Z","timestamp":1791437733335,"version":"4.3.3"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,2,24]],"date-time":"2023-02-24T00:00:00Z","timestamp":1677196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UdS-HIPS TANDEM Interdisciplinary Graduate School for Drug Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Bloom filters are a popular data structure that allows rapid searches in large sequence datasets. So far, all tools work with nucleotide sequences; however, protein sequences are conserved over longer evolutionary distances, and only mutations on the protein level may have any functional significance.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present MetaProFi, a Bloom filter-based tool that, for the first time, offers the functionality to build indexes of amino acid sequences and query them with both amino acid and nucleotide sequences, thus bringing sequence comparison to the biologically relevant protein level. MetaProFi implements additional efficient engineering solutions, such as a shared memory system, chunked data storage and efficient compression. In addition to its conceptual novelty, MetaProFi demonstrates state-of-the-art performance and excellent memory consumption-to-speed ratio when applied to various large datasets.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Source code in Python is available at https:\/\/github.com\/kalininalab\/metaprofi.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad101","type":"journal-article","created":{"date-parts":[[2023,2,24]],"date-time":"2023-02-24T11:36:38Z","timestamp":1677238598000},"source":"Crossref","is-referenced-by-count":12,"title":["MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1752-5060","authenticated-orcid":false,"given":"Sanjay K","family":"Srikakulam","sequence":"first","affiliation":[{"name":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) , 66123 Saarbr\u00fccken, Germany"},{"name":"Graduate School of Computer Science, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Interdisciplinary Graduate School of Natural Product Research, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Keller","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) , 66123 Saarbr\u00fccken, Germany"},{"name":"Graduate School of Computer Science, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fawaz","family":"Dabbaghie","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) , 66123 Saarbr\u00fccken, Germany"},{"name":"Institute for Medical Biometry and Bioinformatics, Heinrich Heine University D\u00fcsseldorf, Medical Faculty , 40225 D\u00fcsseldorf, Germany"},{"name":"Center for Digital Medicine, Heinrich Heine University , 40225 D\u00fcsseldorf, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Bals","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine V\u2014Pulmonology, Allergology, Intensive Care Medicine , 66421 Homburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9445-477X","authenticated-orcid":false,"given":"Olga V","family":"Kalinina","sequence":"additional","affiliation":[{"name":"Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) , 66123 Saarbr\u00fccken, Germany"},{"name":"Drug Bioinformatics, Medical Faculty, Saarland University , 66421 Homburg, Germany"},{"name":"Center for Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,2,24]]},"reference":[{"key":"2023030819152144500_","first-page":"285","author":"Bingmann","year":"2019"},{"key":"2023030819152144500_","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/s41587-018-0010-1","article-title":"Ultrafast search of all deposited bacterial and viral genomic data","volume":"37","author":"Bradley","year":"2019","journal-title":"Nat. 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