{"id":"https://openalex.org/W2171975444","doi":"https://doi.org/10.1093/bioinformatics/bts240","title":"PSI-Search: iterative HOE-reduced profile SSEARCH searching","display_name":"PSI-Search: iterative HOE-reduced profile SSEARCH searching","publication_year":2012,"publication_date":"2012-04-25","ids":{"openalex":"https://openalex.org/W2171975444","doi":"https://doi.org/10.1093/bioinformatics/bts240","mag":"2171975444","pmid":"https://pubmed.ncbi.nlm.nih.gov/22539666"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts240","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1650/48874098/bioinformatics_28_12_1650.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/28/12/1650/48874098/bioinformatics_28_12_1650.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101583301","display_name":"Weizhong Li","orcid":"https://orcid.org/0000-0002-9003-7733"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Weizhong Li","raw_affiliation_strings":["1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084942657","display_name":"Hamish McWilliam","orcid":"https://orcid.org/0000-0003-1769-5032"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hamish McWilliam","raw_affiliation_strings":["1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004495055","display_name":"Mickael Goujon","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mickael Goujon","raw_affiliation_strings":["1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004585203","display_name":"Andrew Cowley","orcid":"https://orcid.org/0000-0001-5092-2220"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrew Cowley","raw_affiliation_strings":["1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018972787","display_name":"Rodrigo L\u00f3pez","orcid":"https://orcid.org/0000-0003-1256-7306"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Rodrigo Lopez","raw_affiliation_strings":["1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073334733","display_name":"William R. Pearson","orcid":"https://orcid.org/0000-0002-0727-3680"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"William R. Pearson","raw_affiliation_strings":["1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 EMBL \u2013 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Department of Biochemistry and Molecular Genetics, Charlottesville, VA 22908, USA","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5018972787","https://openalex.org/A5073334733"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.2499,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.88669525,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"12","first_page":"1650","last_page":"1651"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.3880999982357025,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.3880999982357025,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.29249998927116394,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.06319999694824219,"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/perl","display_name":"Perl","score":0.6590852737426758},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6382922530174255},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.6015905737876892},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.42949363589286804},{"id":"https://openalex.org/keywords/database-search-engine","display_name":"Database search engine","score":0.4142007827758789},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.39515265822410583},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37502312660217285},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.30512967705726624},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22891801595687866},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1682780385017395}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.6590852737426758},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6382922530174255},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.6015905737876892},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.42949363589286804},{"id":"https://openalex.org/C48000682","wikidata":"https://www.wikidata.org/wiki/Q5227411","display_name":"Database search engine","level":3,"score":0.4142007827758789},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.39515265822410583},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37502312660217285},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.30512967705726624},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22891801595687866},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1682780385017395}],"mesh":[{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts240","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1650/48874098/bioinformatics_28_12_1650.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22539666","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22539666","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:europepmc.org:2378089","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3371869","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.827.5746","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.827.5746","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2012/04/24/bioinformatics.bts240.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts240","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts240","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/12/1650/48874098/bioinformatics_28_12_1650.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2618860244","display_name":"Serving Life-science Information for the Next Generation","funder_award_id":"226073","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5015244220","display_name":null,"funder_award_id":"R01 LM004969","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G712632771","display_name":null,"funder_award_id":"LM04969","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320314023","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171975444.pdf","grobid_xml":"https://content.openalex.org/works/W2171975444.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1996423252","https://openalex.org/W2046892081","https://openalex.org/W2069458148","https://openalex.org/W2087064593","https://openalex.org/W2089499735","https://openalex.org/W2107757325","https://openalex.org/W2138122982","https://openalex.org/W2138345179","https://openalex.org/W2139271731","https://openalex.org/W2150483438","https://openalex.org/W2150999244","https://openalex.org/W2154268145","https://openalex.org/W2158714788","https://openalex.org/W2159012716","https://openalex.org/W2162429168","https://openalex.org/W2163120565","https://openalex.org/W2169686324"],"related_works":["https://openalex.org/W230311896","https://openalex.org/W2348885786","https://openalex.org/W2060494738","https://openalex.org/W2367514503","https://openalex.org/W2359370290","https://openalex.org/W2181560882","https://openalex.org/W2372722729","https://openalex.org/W2387206829","https://openalex.org/W2351412568","https://openalex.org/W2187419685"],"abstract_inverted_index":{"UNLABELLED:":[0],"Iterative":[1],"similarity":[2],"searches":[3],"with":[4,44],"PSI-BLAST":[5,46,80,90],"position-specific":[6],"score":[7],"matrices":[8],"(PSSMs)":[9],"find":[10],"many":[11],"more":[12],"homologs":[13],"than":[14,89,109],"single":[15],"searches,":[16],"but":[17,83,111],"PSSMs":[18],"can":[19,66],"be":[20],"contaminated":[21],"when":[22],"homologous":[23],"alignments":[24,57],"are":[25,63],"extended":[26,60],"into":[27],"unrelated":[28],"protein":[29],"domains-homologous":[30],"over-extension":[31],"(HOE).":[32],"PSI-Search":[33,84,100,119],"combines":[34],"an":[35],"optimal":[36],"Smith-Waterman":[37],"local":[38],"alignment":[39],"sequence":[40,52],"search,":[41],"using":[42],"SSEARCH,":[43],"the":[45,71,123],"profile":[47],"construction":[48],"strategy.":[49],"An":[50],"optional":[51],"boundary-masking":[53],"procedure,":[54],"which":[55],"prevents":[56],"from":[58,122],"being":[59],"after":[61],"they":[62],"initially":[64],"included,":[65],"reduce":[67],"HOE":[68,75],"errors":[69],"in":[70,130],"PSSM":[72],"profile.":[73],"Preventing":[74],"improves":[76],"selectivity":[77,88],"for":[78,105,132],"both":[79],"and":[81,91,96,144,146],"PSI-Search,":[82],"has":[85],"~4-fold":[86],"better":[87],"similar":[92],"sensitivity":[93],"at":[94],"50%":[95],"60%":[97],"family":[98],"coverage.":[99],"is":[101,112,120,136],"also":[102,137],"produces":[103],"2-":[104],"4-fold":[106],"fewer":[107],"false-positives":[108],"JackHMMER,":[110],"~5%":[113],"less":[114],"sensitive.":[115],"AVAILABILITY":[116],"AND":[117],"IMPLEMENTATION:":[118],"available":[121,138],"authors":[124],"as":[125],"a":[126,140],"standalone":[127],"implementation":[128],"written":[129],"Perl":[131],"Linux-compatible":[133],"platforms.":[134],"It":[135],"through":[139],"web":[141],"interface":[142],"(www.ebi.ac.uk/Tools/sss/psisearch)":[143],"SOAP":[145],"REST":[147],"Web":[148],"Services":[149],"(www.ebi.ac.uk/Tools/webservices).":[150]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
