{"id":"https://openalex.org/W2096760403","doi":"https://doi.org/10.1093/bioinformatics/btp087","title":"PASS: a program to align short sequences","display_name":"PASS: a program to align short sequences","publication_year":2009,"publication_date":"2009-02-13","ids":{"openalex":"https://openalex.org/W2096760403","doi":"https://doi.org/10.1093/bioinformatics/btp087","mag":"2096760403","pmid":"https://pubmed.ncbi.nlm.nih.gov/19218350"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/967/556767/btp087.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/967/556767/btp087.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050677276","display_name":"Davide Campagna","orcid":"https://orcid.org/0000-0001-8440-0121"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Davide Campagna","raw_affiliation_strings":["CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109121155","display_name":"Alessandro Albiero","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessandro Albiero","raw_affiliation_strings":["CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085622073","display_name":"Alessandra Bilardi","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessandra Bilardi","raw_affiliation_strings":["CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038747013","display_name":"Elisa Caniato","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Elisa Caniato","raw_affiliation_strings":["CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051265127","display_name":"Claudio Forcato","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudio Forcato","raw_affiliation_strings":["CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053446077","display_name":"Svetlin A. Manavski","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Svetlin Manavski","raw_affiliation_strings":["CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019203087","display_name":"Nicola Vitulo","orcid":"https://orcid.org/0000-0002-9571-0747"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nicola Vitulo","raw_affiliation_strings":["CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005828835","display_name":"Giorgio Valle","orcid":"https://orcid.org/0000-0003-4377-5685"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giorgio Valle","raw_affiliation_strings":["CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"CRIBI Biotechnology Centre, University of Padua, via Ugo Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5050677276"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.7392,"has_fulltext":false,"cited_by_count":124,"citation_normalized_percentile":{"value":0.97644204,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"25","issue":"7","first_page":"967","last_page":"968"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9934999942779541,"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/computer-science","display_name":"Computer science","score":0.808708906173706},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.6089390516281128},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5229971408843994},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.511790931224823},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.46712619066238403},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.44525203108787537},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4212827980518341},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39858293533325195},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.2690053880214691},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19227883219718933},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17438486218452454},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13746920228004456},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11312353610992432},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10800042748451233}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.808708906173706},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.6089390516281128},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5229971408843994},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.511790931224823},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.46712619066238403},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.44525203108787537},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4212827980518341},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39858293533325195},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.2690053880214691},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19227883219718933},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17438486218452454},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13746920228004456},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11312353610992432},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10800042748451233},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/967/556767/btp087.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19218350","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19218350","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":null},{"id":"pmh:oai:www.research.unipd.it:11577/2446868","is_oa":true,"landing_page_url":"http://hdl.handle.net/11577/2446868","pdf_url":null,"source":{"id":"https://openalex.org/S4377196283","display_name":"Research Padua  Archive (University of Padua)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/7/967/556767/btp087.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096760403.pdf","grobid_xml":"https://content.openalex.org/works/W2096760403.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2011652244","https://openalex.org/W2015292449","https://openalex.org/W2055043387","https://openalex.org/W2072193858","https://openalex.org/W2074231493","https://openalex.org/W2097862362","https://openalex.org/W2112113834","https://openalex.org/W2123364539","https://openalex.org/W2135809805","https://openalex.org/W2136145671","https://openalex.org/W2139760555","https://openalex.org/W2142619120","https://openalex.org/W2143124024","https://openalex.org/W2164631010","https://openalex.org/W4293196852","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W2378757965","https://openalex.org/W1972035260","https://openalex.org/W4224903346","https://openalex.org/W1593262897","https://openalex.org/W2372869593","https://openalex.org/W2384194537","https://openalex.org/W2031011156","https://openalex.org/W1991935520","https://openalex.org/W2368745429","https://openalex.org/W2348534359"],"abstract_inverted_index":{"Source":[0],"code":[1],"and":[2,17],"binaries":[3],"are":[4],"freely":[5],"available":[6],"for":[7],"download":[8],"at":[9],"http://pass.cribi.unipd.it,":[10],"implemented":[11],"in":[12],"C++and":[13],"supported":[14],"on":[15],"Linux":[16],"Windows.":[18]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":11}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
