{"id":"https://openalex.org/W2123317029","doi":"https://doi.org/10.1093/bioinformatics/bti035","title":"tPatternHunter: gapped, fast and sensitive translated homology search","display_name":"tPatternHunter: gapped, fast and sensitive translated homology search","publication_year":2004,"publication_date":"2004-09-16","ids":{"openalex":"https://openalex.org/W2123317029","doi":"https://doi.org/10.1093/bioinformatics/bti035","mag":"2123317029","pmid":"https://pubmed.ncbi.nlm.nih.gov/15374861"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti035","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/4/542/48965065/bioinformatics_21_4_542.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/4/542/48965065/bioinformatics_21_4_542.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063409642","display_name":"Derek Kisman","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109217","display_name":"Bioinformatics Solutions (Canada)","ror":"https://ror.org/01jzb6k09","country_code":"CA","type":"company","lineage":["https://openalex.org/I4210109217"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Derek Kisman","raw_affiliation_strings":["Bioinformatics Solutions Inc. 145 Columbia St West, Waterloo, Ontario, Canada N2L 3L2","Bioinformatics Solutions Inc. 145 Columbia St West, Waterloo, Ontario, Canada N2L 3L2#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Solutions Inc. 145 Columbia St West, Waterloo, Ontario, Canada N2L 3L2","institution_ids":["https://openalex.org/I4210109217"]},{"raw_affiliation_string":"Bioinformatics Solutions Inc. 145 Columbia St West, Waterloo, Ontario, Canada N2L 3L2#TAB#","institution_ids":["https://openalex.org/I4210109217"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100351326","display_name":"Ming Li","orcid":"https://orcid.org/0000-0001-7049-8666"},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ming Li","raw_affiliation_strings":["School of Computer Science, University of Waterloo                Ontario, Canada N2L 3G1"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Waterloo                Ontario, Canada N2L 3G1","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100749729","display_name":"Bin Ma","orcid":"https://orcid.org/0000-0001-7649-6696"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Bin Ma","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7#TAB#","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100336217","display_name":"Li Wang","orcid":"https://orcid.org/0000-0003-3029-5367"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Li Wang","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7#TAB#","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5063409642"],"corresponding_institution_ids":["https://openalex.org/I4210109217"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.5841,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.8191236,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"21","issue":"4","first_page":"542","last_page":"544"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.993399977684021,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9926999807357788,"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/software","display_name":"Software","score":0.7156175374984741},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7033151388168335},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.69828200340271},{"id":"https://openalex.org/keywords/frame","display_name":"Frame (networking)","score":0.5103868842124939},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4902947247028351},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3819084167480469},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35550457239151},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3208514451980591},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3039008677005768},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1861344873905182},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1348760426044464},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.060044050216674805},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.05416342616081238}],"concepts":[{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.7156175374984741},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7033151388168335},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.69828200340271},{"id":"https://openalex.org/C126042441","wikidata":"https://www.wikidata.org/wiki/Q1324888","display_name":"Frame (networking)","level":2,"score":0.5103868842124939},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4902947247028351},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3819084167480469},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35550457239151},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3208514451980591},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3039008677005768},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1861344873905182},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1348760426044464},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.060044050216674805},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.05416342616081238},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti035","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/4/542/48965065/bioinformatics_21_4_542.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15374861","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15374861","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Evaluation Study"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti035","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/4/542/48965065/bioinformatics_21_4_542.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320994","display_name":"Canada Research Chairs","ror":"https://ror.org/0517h6h17"},{"id":"https://openalex.org/F4320322337","display_name":"Killam Trusts","ror":"https://ror.org/021cbtn85"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2123317029.pdf"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W631149005","https://openalex.org/W1518052104","https://openalex.org/W1955121107","https://openalex.org/W2055043387","https://openalex.org/W2128591967","https://openalex.org/W2131989567","https://openalex.org/W2158714788","https://openalex.org/W2476317680"],"related_works":["https://openalex.org/W323219885","https://openalex.org/W4292559016","https://openalex.org/W4231937131","https://openalex.org/W1589342014","https://openalex.org/W598950423","https://openalex.org/W2778913187","https://openalex.org/W4256673449","https://openalex.org/W1980419027","https://openalex.org/W2143331802","https://openalex.org/W2160964171"],"abstract_inverted_index":{"UNLABELLED:":[0],"New":[1],"ideas,":[2],"spaced":[3],"seeds":[4],"and":[5],"gapped":[6],"alignment":[7],"before":[8],"6-frame":[9],"translation":[10],"are":[11],"implemented":[12],"for":[13],"translated":[14],"homology":[15],"search":[16],"in":[17],"tPatternHunter.":[18],"The":[19,27],"new":[20],"software":[21,28],"compares":[22],"favorably":[23],"with":[24],"tBLASTx.":[25],"AVAILABILITY:":[26],"is":[29],"free":[30],"to":[31],"academics":[32],"at":[33],"http://www.bioinformaticssolutions.com/downloads/ph-academic/":[34],"CONTACT:":[35],"bma@csd.uwo.ca.":[36]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
