{"id":"https://openalex.org/W2118836759","doi":"https://doi.org/10.1093/bioinformatics/btg185","title":"Probabilistic scoring measures for profile\u2013profilecomparison yield more accurate short seed alignments","display_name":"Probabilistic scoring measures for profile\u2013profilecomparison yield more accurate short seed alignments","publication_year":2003,"publication_date":"2003-08-11","ids":{"openalex":"https://openalex.org/W2118836759","doi":"https://doi.org/10.1093/bioinformatics/btg185","mag":"2118836759","pmid":"https://pubmed.ncbi.nlm.nih.gov/12912834"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg185","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg185","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062071800","display_name":"David Mittelman","orcid":"https://orcid.org/0009-0008-6087-6617"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"education","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David Mittelman","raw_affiliation_strings":["Howard Hughes Medical Institute Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA","University of Texas, Southwestern Medical Center"],"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA","institution_ids":[]},{"raw_affiliation_string":"University of Texas, Southwestern Medical Center","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014184589","display_name":"Ruslan I. Sadreyev","orcid":"https://orcid.org/0000-0002-4240-5466"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"education","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruslan Sadreyev","raw_affiliation_strings":["University of Texas, Southwestern Medical Center"],"affiliations":[{"raw_affiliation_string":"University of Texas, Southwestern Medical Center","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108096094","display_name":"Nick V. Grishin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nick Grishin","raw_affiliation_strings":["Biochemistry"],"affiliations":[{"raw_affiliation_string":"Biochemistry","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5062071800"],"corresponding_institution_ids":["https://openalex.org/I867280407"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.2184,"has_fulltext":false,"cited_by_count":75,"citation_normalized_percentile":{"value":0.92575954,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"19","issue":"12","first_page":"1531","last_page":"1539"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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":0.9980000257492065,"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":0.983299970626831,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9825999736785889,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.726057767868042},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6876355409622192},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5098461508750916},{"id":"https://openalex.org/keywords/compass","display_name":"Compass","score":0.4765739440917969},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46196362376213074},{"id":"https://openalex.org/keywords/basis","display_name":"Basis (linear algebra)","score":0.45515531301498413},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4019727408885956},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36423346400260925},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3426061272621155},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22434192895889282},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.08861875534057617}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.726057767868042},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6876355409622192},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5098461508750916},{"id":"https://openalex.org/C2778361833","wikidata":"https://www.wikidata.org/wiki/Q34735","display_name":"Compass","level":2,"score":0.4765739440917969},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46196362376213074},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.45515531301498413},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4019727408885956},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36423346400260925},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3426061272621155},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22434192895889282},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.08861875534057617},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg185","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg185","pdf_url":null,"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:12912834","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12912834","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1590648220","https://openalex.org/W1986014242","https://openalex.org/W1996159969","https://openalex.org/W2009570821","https://openalex.org/W2028654361","https://openalex.org/W2036295979","https://openalex.org/W2055043387","https://openalex.org/W2060791849","https://openalex.org/W2062693912","https://openalex.org/W2068083406","https://openalex.org/W2087064593","https://openalex.org/W2097874946","https://openalex.org/W2099075703","https://openalex.org/W2102122585","https://openalex.org/W2117249420","https://openalex.org/W2124145810","https://openalex.org/W2139621307","https://openalex.org/W2147667050","https://openalex.org/W2151831732","https://openalex.org/W2158714788","https://openalex.org/W2166325055","https://openalex.org/W2167257571"],"related_works":["https://openalex.org/W2206872286","https://openalex.org/W2382913035","https://openalex.org/W2391335452","https://openalex.org/W2113447385","https://openalex.org/W2360876323","https://openalex.org/W2109954054","https://openalex.org/W2642723128","https://openalex.org/W1970764900","https://openalex.org/W2366280361","https://openalex.org/W638953695"],"abstract_inverted_index":{"Our":[0],"results":[1],"suggest":[2],"that":[3],"the":[4,7,17,22,28,42,51],"family":[5],"of":[6,24,46],"probabilistic":[8],"methods":[9,12],"(log-odds":[10],"based":[11],"and":[13,53],"prof_sim)":[14],"may":[15],"be":[16],"more":[18],"appropriate":[19],"choice":[20],"for":[21],"generation":[23],"initial":[25],"'seeds'":[26],"as":[27],"first":[29],"step":[30],"to":[31],"produce":[32],"local":[33],"profile-profile":[34],"alignments.":[35],"The":[36],"most":[37],"effective":[38],"scoring":[39],"systems":[40],"were":[41],"closely":[43],"related":[44],"modifications":[45],"functions":[47],"previously":[48],"implemented":[49],"in":[50],"COMPASS":[52],"Picasso":[54],"methods.":[55]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}