{"id":"https://openalex.org/W7117464210","doi":"https://doi.org/10.3390/a19010030","title":"Comparison of Online Searching Algorithms for IUPAC Nucleotide Sequences","display_name":"Comparison of Online Searching Algorithms for IUPAC Nucleotide Sequences","publication_year":2025,"publication_date":"2025-12-29","ids":{"openalex":"https://openalex.org/W7117464210","doi":"https://doi.org/10.3390/a19010030"},"language":"en","primary_location":{"id":"doi:10.3390/a19010030","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a19010030","pdf_url":"https://www.mdpi.com/1999-4893/19/1/30/pdf?version=1766986443","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/19/1/30/pdf?version=1766986443","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033294598","display_name":"Jorma Tarhio","orcid":"https://orcid.org/0000-0003-2455-1985"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Jorma Tarhio","raw_affiliation_strings":["Department of Computer Science, Aalto University, P.O. Box 1540, FI-00076 Aalto, Finland"],"raw_orcid":"https://orcid.org/0000-0003-2455-1985","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University, P.O. Box 1540, FI-00076 Aalto, Finland","institution_ids":["https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5033294598"],"corresponding_institution_ids":["https://openalex.org/I9927081"],"apc_list":{"value":1600,"currency":"CHF","value_usd":1782},"apc_paid":{"value":1600,"currency":"CHF","value_usd":1782},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.78284844,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"19","issue":"1","first_page":"30","last_page":"30"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.335999995470047,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.335999995470047,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.06880000233650208,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.061400000005960464,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5911999940872192},{"id":"https://openalex.org/keywords/simd","display_name":"SIMD","score":0.5881999731063843},{"id":"https://openalex.org/keywords/chemical-nomenclature","display_name":"Chemical nomenclature","score":0.5570999979972839},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.47049999237060547},{"id":"https://openalex.org/keywords/degenerate-energy-levels","display_name":"Degenerate energy levels","score":0.4004000127315521},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.3382999897003174}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6714000105857849},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5911999940872192},{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.5881999731063843},{"id":"https://openalex.org/C125832229","wikidata":"https://www.wikidata.org/wiki/Q6503924","display_name":"Chemical nomenclature","level":2,"score":0.5570999979972839},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5217999815940857},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.47049999237060547},{"id":"https://openalex.org/C72319582","wikidata":"https://www.wikidata.org/wiki/Q584304","display_name":"Degenerate energy levels","level":2,"score":0.4004000127315521},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34689998626708984},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.3382999897003174},{"id":"https://openalex.org/C39613435","wikidata":"https://www.wikidata.org/wiki/Q846677","display_name":"Remainder","level":2,"score":0.335999995470047},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.33480000495910645},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3075999915599823},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.26600000262260437},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.2526000142097473}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/a19010030","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a19010030","pdf_url":"https://www.mdpi.com/1999-4893/19/1/30/pdf?version=1766986443","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:284190b2ee8b4c11a492de3782c71e40","is_oa":true,"landing_page_url":"https://doaj.org/article/284190b2ee8b4c11a492de3782c71e40","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms, Vol 19, Iss 1, p 30 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/a19010030","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a19010030","pdf_url":"https://www.mdpi.com/1999-4893/19/1/30/pdf?version=1766986443","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7117464210.pdf","grobid_xml":"https://content.openalex.org/works/W7117464210.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1519856633","https://openalex.org/W1968655052","https://openalex.org/W1976978590","https://openalex.org/W1978173716","https://openalex.org/W1983788629","https://openalex.org/W2092587157","https://openalex.org/W2559879471","https://openalex.org/W4302036977","https://openalex.org/W4393987724","https://openalex.org/W4408359848"],"related_works":[],"abstract_inverted_index":{"We":[0,10],"consider":[1],"online":[2],"pattern":[3],"matching":[4],"algorithms":[5,17],"for":[6,34,39],"IUPAC":[7,57],"nucleotide":[8],"sequences.":[9,58],"present":[11],"an":[12],"experimental":[13],"comparison":[14],"of":[15],"search":[16,56],"while":[18],"allowing":[19],"3%":[20],"degenerate":[21],"symbols.":[22],"In":[23],"addition,":[24],"we":[25],"introduce":[26],"two":[27],"new":[28],"algorithms,":[29],"one":[30],"utilizing":[31],"SIMD":[32],"instructions":[33],"short":[35],"patterns":[36],"and":[37],"another":[38],"long":[40],"patterns.":[41],"A":[42],"BNDM":[43],"variation":[44],"with":[45],"6-grams":[46],"turned":[47],"out":[48],"to":[49,55],"be":[50],"the":[51],"best":[52],"general":[53],"method":[54]},"counts_by_year":[],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-12-29T00:00:00"}
