{"id":"https://openalex.org/W2145268834","doi":"https://doi.org/10.1093/bioinformatics/bti125","title":"Protein homology detection by HMM\u2013HMM comparison","display_name":"Protein homology detection by HMM\u2013HMM comparison","publication_year":2004,"publication_date":"2004-11-05","ids":{"openalex":"https://openalex.org/W2145268834","doi":"https://doi.org/10.1093/bioinformatics/bti125","mag":"2145268834","pmid":"https://pubmed.ncbi.nlm.nih.gov/15531603"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti125","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti125","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/951/48966807/bioinformatics_21_7_951.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/21/7/951/48966807/bioinformatics_21_7_951.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010030898","display_name":"Johannes S\u00f6ding","orcid":"https://orcid.org/0000-0001-9642-8244"},"institutions":[{"id":"https://openalex.org/I4210112458","display_name":"Max Planck Institute for Developmental Biology","ror":"https://ror.org/022jc0g24","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210112458"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Johannes S\u00f6ding","raw_affiliation_strings":["Department of Protein Evolution, Max-Planck-Institute for Developmental Biology Spemannstrasse 35, D-72076 T\u00fcbingen, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Protein Evolution, Max-Planck-Institute for Developmental Biology Spemannstrasse 35, D-72076 T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I4210112458"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5010030898"],"corresponding_institution_ids":["https://openalex.org/I4210112458"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":13.9877,"has_fulltext":true,"cited_by_count":2504,"citation_normalized_percentile":{"value":0.99488036,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"21","issue":"7","first_page":"951","last_page":"960"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9986000061035156,"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":0.9983000159263611,"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/hidden-markov-model","display_name":"Hidden Markov model","score":0.877010703086853},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.6730021238327026},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.6043124794960022},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.571958065032959},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.528169572353363},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.5165795087814331},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.5112121105194092},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.4831225574016571},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.47947725653648376},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.47719916701316833},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4208422303199768},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4017244875431061},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37168192863464355},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36323344707489014},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3611398935317993},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.18961337208747864},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.18407869338989258},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14972540736198425}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.877010703086853},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.6730021238327026},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.6043124794960022},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.571958065032959},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.528169572353363},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.5165795087814331},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.5112121105194092},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.4831225574016571},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.47947725653648376},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.47719916701316833},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4208422303199768},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4017244875431061},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37168192863464355},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36323344707489014},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3611398935317993},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.18961337208747864},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.18407869338989258},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14972540736198425},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"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":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":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":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bti125","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti125","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/951/48966807/bioinformatics_21_7_951.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:15531603","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15531603","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:pure.mpg.de:item_1944253","is_oa":true,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0017-EC7A-F","pdf_url":"http://hdl.handle.net/11858/00-001M-0000-0017-EC7A-F","source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.519.1257","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.519.1257","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/2004/11/05/bioinformatics.bti125.full.pdf","raw_type":"text"},{"id":"pmh:oai:edoc.mpg.de:222515","is_oa":false,"landing_page_url":"http://edoc.mpg.de/222515","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, v.21, 951-960 (2005)","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti125","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti125","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/7/951/48966807/bioinformatics_21_7_951.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":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2145268834.pdf","grobid_xml":"https://content.openalex.org/works/W2145268834.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W196133890","https://openalex.org/W1590648220","https://openalex.org/W1963726977","https://openalex.org/W1970999032","https://openalex.org/W1971751969","https://openalex.org/W2004575181","https://openalex.org/W2005313213","https://openalex.org/W2008708467","https://openalex.org/W2008922668","https://openalex.org/W2009570821","https://openalex.org/W2015292449","https://openalex.org/W2017668812","https://openalex.org/W2028654361","https://openalex.org/W2036792999","https://openalex.org/W2036928610","https://openalex.org/W2045564656","https://openalex.org/W2051969447","https://openalex.org/W2055043387","https://openalex.org/W2057447180","https://openalex.org/W2060791849","https://openalex.org/W2062693912","https://openalex.org/W2084466582","https://openalex.org/W2085277871","https://openalex.org/W2098487344","https://openalex.org/W2099075703","https://openalex.org/W2102122585","https://openalex.org/W2102677343","https://openalex.org/W2106241755","https://openalex.org/W2106882534","https://openalex.org/W2109806386","https://openalex.org/W2110534451","https://openalex.org/W2118836759","https://openalex.org/W2129913453","https://openalex.org/W2133270255","https://openalex.org/W2133657429","https://openalex.org/W2142513984","https://openalex.org/W2147667050","https://openalex.org/W2149758239","https://openalex.org/W2151631782","https://openalex.org/W2151831732","https://openalex.org/W2151904894","https://openalex.org/W2153187042","https://openalex.org/W2153414768","https://openalex.org/W2157938277","https://openalex.org/W2158714788","https://openalex.org/W2158749079","https://openalex.org/W2164652663","https://openalex.org/W2164864731","https://openalex.org/W2168508791","https://openalex.org/W2169459078","https://openalex.org/W2170962128","https://openalex.org/W4245668478","https://openalex.org/W4253986630"],"related_works":["https://openalex.org/W2948014085","https://openalex.org/W2004215917","https://openalex.org/W2103737249","https://openalex.org/W2051969447","https://openalex.org/W1486249959","https://openalex.org/W1974956921","https://openalex.org/W2468116983","https://openalex.org/W2146180248","https://openalex.org/W2111937814","https://openalex.org/W4386770652"],"abstract_inverted_index":{"We":[0,24],"have":[1],"generalized":[2],"the":[3,16,50,78,85,125,128,135,170,185],"alignment":[4,20,154],"of":[5,18,21,61,64,117,120,124,137,142,196],"protein":[6,66],"sequences":[7],"with":[8,45,71],"a":[9,26,62,115,194],"profile":[10,22,138],"hidden":[11],"Markov":[12],"model":[13],"(HMM)":[14],"to":[15,90,134],"case":[17],"pairwise":[19,72],"HMMs.":[23],"present":[25],"method":[27,40,173],"for":[28,114],"detecting":[29],"distant":[30],"homologous":[31],"relationships":[32],"between":[33,92,104],"proteins":[34],"based":[35],"on":[36,205],"this":[37],"approach.":[38],"The":[39],"(HHsearch)":[41],"is":[42,82,88,132,149,211],"benchmarked":[43],"together":[44],"BLAST,":[46],"PSI-BLAST,":[47,183],"HMMER":[48,102],"and":[49,55,94,103,106,160,175,178,188,217],"profile-profile":[51,129],"comparison":[52,60,130],"tools":[53],"PROF_SIM":[54,113,216],"COMPASS,":[56],"in":[57,84,140,202],"an":[58,152,206],"all-against-all":[59],"database":[63],"3691":[65,200],"domains":[67,201],"from":[68],"SCOP":[69],"1.63":[70],"sequence":[73],"identities":[74],"below":[75],"20%.Sensitivity:":[76],"When":[77],"predicted":[79],"secondary":[80],"structure":[81],"included":[83],"HMMs,":[86],"HHsearch":[87,156,192],"able":[89],"detect":[91],"2.7":[93],"4.2":[95],"times":[96,108,162,180,213,219],"more":[97,109,163,181],"homologs":[98],"than":[99,110,169,182,215,221],"PSI-BLAST":[100],"or":[101,112],"1.44":[105],"1.9":[107],"COMPASS":[111],"rate":[116],"false":[118],"positives":[119],"10%.":[121],"Approximately":[122],"half":[123],"improvement":[126],"over":[127],"methods":[131],"attributable":[133],"use":[136],"HMMs":[139],"place":[141],"simple":[143],"profiles.":[144],"Alignment":[145],"quality:":[146],"Higher":[147],"sensitivity":[148],"mirrored":[150],"by":[151],"increased":[153],"quality.":[155],"produced":[157],"1.2,":[158],"1.7":[159],"3.3":[161],"good":[164],"alignments":[165],"('balanced'":[166],"score":[167],">0.3)":[168],"next":[171],"best":[172],"(COMPASS),":[174],"1.6,":[176],"2.9":[177],"9.4":[179],"at":[184],"family,":[186],"superfamily":[187],"fold":[189],"level,":[190],"respectively.Speed:":[191],"scans":[193],"query":[195],"200":[197],"residues":[198],"against":[199],"33":[203],"s":[204],"AMD64":[207],"2GHz":[208],"PC.":[209],"This":[210],"10":[212],"faster":[214,220],"17":[218],"COMPASS.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":58},{"year":2024,"cited_by_count":90},{"year":2023,"cited_by_count":94},{"year":2022,"cited_by_count":150},{"year":2021,"cited_by_count":168},{"year":2020,"cited_by_count":149},{"year":2019,"cited_by_count":156},{"year":2018,"cited_by_count":137},{"year":2017,"cited_by_count":168},{"year":2016,"cited_by_count":163},{"year":2015,"cited_by_count":169},{"year":2014,"cited_by_count":156},{"year":2013,"cited_by_count":175},{"year":2012,"cited_by_count":135}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}