{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T06:34:25Z","timestamp":1766990065390,"version":"3.48.0"},"reference-count":14,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T00:00:00Z","timestamp":1766966400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Algorithms"],"abstract":"<jats:p>We consider online pattern matching algorithms for IUPAC nucleotide sequences. We present an experimental comparison of search algorithms while allowing 3% degenerate symbols. In addition, we introduce two new algorithms, one utilizing SIMD instructions for short patterns and another for long patterns. A BNDM variation with 6-grams turned out to be the best general method to search IUPAC sequences.<\/jats:p>","DOI":"10.3390\/a19010030","type":"journal-article","created":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T06:25:51Z","timestamp":1766989551000},"page":"30","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparison of Online Searching Algorithms for IUPAC Nucleotide Sequences"],"prefix":"10.3390","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2455-1985","authenticated-orcid":false,"given":"Jorma","family":"Tarhio","sequence":"first","affiliation":[{"name":"Department of Computer Science, Aalto University, P.O. Box 1540, FI-00076 Aalto, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.1093\/nar\/13.9.3021","article-title":"Nomenclature for incompletely specified bases in nucleic acid sequences: Recommendations 1984","volume":"13","year":"1985","journal-title":"Nucleic Acids Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/2431211.2431212","article-title":"The exact online string matching problem: A review of the most recent results","volume":"45","author":"Faro","year":"2013","journal-title":"ACM Comput. Surv."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Farach-Colton, M. (1998). A bit-parallel approach to suffix automata: Fast extended string matching. Annual Symposium on Combinatorial Pattern Matching, Springer.","DOI":"10.1007\/BFb0030776"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.ipl.2009.11.010","article-title":"Improving practical exact string matching","volume":"110","author":"Holub","year":"2010","journal-title":"Inf. Process. Lett."},{"key":"ref_5","unstructured":"Maria, E.D., Fred, A.L.N., and Gamboa, H. (2019, January 22\u201324). On-line searching in IUPAC nucleotide sequences. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2019)\u2014Volume 3: BIOINFORMATICS, Prague, Czech Republic."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2160","DOI":"10.1002\/spe.3335","article-title":"Searching long patterns with BNDM","volume":"54","author":"Tarhio","year":"2024","journal-title":"Softw. Pract. Exp."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.dam.2025.02.032","article-title":"Practical KMP\/BM style pattern-matching on indeterminate strings","volume":"370","author":"Dehghani","year":"2025","journal-title":"Discret. Appl. Math."},{"key":"ref_8","unstructured":"Holub, J., and Smyth, W.F. (2003, January 13\u201316). Algorithms on indeterminate strings. Proceedings of the 14th Australasian Workshop on Combinatorial Algorithms, AWOCA, Seoul, Republic of Korea."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1145\/351827.384246","article-title":"Fast and flexible string matching by combining bit-parallelism and suffix automata","volume":"5","author":"Navarro","year":"2000","journal-title":"ACM J. Exp. Algorithmics"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1007\/978-3-540-39984-1_7","article-title":"Alternative algorithms for bit-parallel string matching","volume":"Volume 2857","author":"Nascimento","year":"2003","journal-title":"String Processing and Information Retrieval. SPIRE 2003"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.1002\/spe.2511","article-title":"Technology beats algorithms (in exact string matching)","volume":"47","author":"Tarhio","year":"2017","journal-title":"Softw. Pract. Exp."},{"key":"ref_12","unstructured":"Intel (2025, June 11). Intel Intrinsics Guide. Available online: https:\/\/www.intel.com\/content\/www\/us\/en\/docs\/intrinsics-guide\/index.html#."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1002\/spe.4380211105","article-title":"Fast string searching","volume":"21","author":"Hume","year":"1991","journal-title":"Softw. Pract. Exp."},{"key":"ref_14","unstructured":"Holub, J., and Zd\u00e1rek, J. (2021). Pitfalls of algorithm comparison. Prague Stringology Conference 2021, Czech Technical University."}],"container-title":["Algorithms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4893\/19\/1\/30\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T06:31:05Z","timestamp":1766989865000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4893\/19\/1\/30"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,29]]},"references-count":14,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["a19010030"],"URL":"https:\/\/doi.org\/10.3390\/a19010030","relation":{},"ISSN":["1999-4893"],"issn-type":[{"value":"1999-4893","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,29]]}}}