{"id":"https://openalex.org/W2125555860","doi":"https://doi.org/10.1093/bioinformatics/btg485","title":"Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs","display_name":"Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs","publication_year":2004,"publication_date":"2004-01-29","ids":{"openalex":"https://openalex.org/W2125555860","doi":"https://doi.org/10.1093/bioinformatics/btg485","mag":"2125555860","pmid":"https://pubmed.ncbi.nlm.nih.gov/14751996"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg485","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/6/818/48905151/bioinformatics_20_6_818.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/20/6/818/48905151/bioinformatics_20_6_818.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014184589","display_name":"Ruslan I. Sadreyev","orcid":"https://orcid.org/0000-0002-4240-5466"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ruslan I. Sadreyev","raw_affiliation_strings":["Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108096094","display_name":"Nick V. Grishin","orcid":null},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nick V. Grishin","raw_affiliation_strings":["Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, and Department of Biochemistry, University of Texas Southwestern Medical Center, 5323, Harry Hines Blvd, Dallas, TX 75390-9050, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014184589"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0203,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.73766991,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"6","first_page":"818","last_page":"828"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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":0.9973999857902527,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9686999917030334,"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/diversity","display_name":"Diversity (politics)","score":0.7623589038848877},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6892834901809692},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6866214871406555},{"id":"https://openalex.org/keywords/compass","display_name":"Compass","score":0.6502267122268677},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.5895077586174011},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4987518787384033},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47997188568115234},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4748055040836334},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.46598783135414124},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.403203547000885},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3605760931968689},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.33274856209754944},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30589088797569275},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.18300142884254456},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.13520032167434692},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.13000306487083435},{"id":"https://openalex.org/keywords/cartography","display_name":"Cartography","score":0.09367808699607849},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08364075422286987},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.06590837240219116}],"concepts":[{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.7623589038848877},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6892834901809692},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6866214871406555},{"id":"https://openalex.org/C2778361833","wikidata":"https://www.wikidata.org/wiki/Q34735","display_name":"Compass","level":2,"score":0.6502267122268677},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.5895077586174011},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4987518787384033},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47997188568115234},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4748055040836334},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.46598783135414124},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.403203547000885},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3605760931968689},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33274856209754944},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30589088797569275},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.18300142884254456},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.13520032167434692},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.13000306487083435},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.09367808699607849},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08364075422286987},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06590837240219116},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","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":"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},{"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},{"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/btg485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg485","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/6/818/48905151/bioinformatics_20_6_818.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:14751996","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14751996","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:CiteSeerX.psu:10.1.1.543.7374","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.543.7374","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/2004/01/29/bioinformatics.btg485.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.589.2204","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.589.2204","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/20/6/818.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg485","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/6/818/48905151/bioinformatics_20_6_818.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":[{"id":"https://metadata.un.org/sdg/10","score":0.6200000047683716,"display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2125555860.pdf","grobid_xml":"https://content.openalex.org/works/W2125555860.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1590648220","https://openalex.org/W1977922844","https://openalex.org/W2021953523","https://openalex.org/W2028654361","https://openalex.org/W2045564656","https://openalex.org/W2050956531","https://openalex.org/W2062693912","https://openalex.org/W2099075703","https://openalex.org/W2117249420","https://openalex.org/W2118836759","https://openalex.org/W2124145810","https://openalex.org/W2133312664","https://openalex.org/W2139621307","https://openalex.org/W2140244239","https://openalex.org/W2141885858","https://openalex.org/W2147667050","https://openalex.org/W2149758239","https://openalex.org/W2151631782","https://openalex.org/W2151831732","https://openalex.org/W2158714788","https://openalex.org/W2163181687","https://openalex.org/W2167257571","https://openalex.org/W4210531204"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2141411672"],"abstract_inverted_index":{"MOTIVATION:":[0],"Adding":[1],"more":[2,133,138],"distant":[3,117],"homologs":[4,42,79,205],"to":[5,161,173,210],"a":[6,31,73,144],"multiple":[7,199],"alignment":[8,109,200],"and":[9,46],"thus":[10],"increasing":[11],"its":[12],"diversity":[13,32,64,146],"may":[14],"eventually":[15],"deteriorate":[16],"the":[17,27,38,49,52,55,62,81,115,128,130,150,177,198,212],"numerical":[18],"profile":[19,93,154,192],"constructed":[20],"from":[21,124],"this":[22],"alignment.":[23],"Here,":[24],"we":[25,47],"addressed":[26],"question":[28],"whether":[29],"such":[30],"limit":[33],"can":[34],"be":[35,112,162,174],"reached":[36],"in":[37,80,92,137,197,208],"alignments":[39,102,155],"of":[40,51,54,76,89,119,132,147,153,165,180,191],"confident":[41,78,148,203],"found":[43],"by":[44,59,176],"PSI-BLAST,":[45],"analyzed":[48],"dependence":[50],"quality":[53,88,152],"profile-profile":[56,101],"comparison":[57],"made":[58],"COMPASS":[60],"on":[61,97],"sequence":[63,83,204],"within":[65],"these":[66,120,166],"alignments.":[67,140],"RESULTS:":[68],"Protein":[69],"families":[70,121,142,167],"that":[71,187],"have":[72],"greater":[74],"number":[75,179],"diverse":[77,134,181],"current":[82],"databases":[84],"provide":[85],"an":[86,163],"increased":[87],"similarity":[90],"detection":[91],"databases,":[94],"but":[95],"produce":[96,211],"average":[98],"less":[99],"accurate":[100,139,214],"with":[103,143,156],"their":[104,125,157,169],"remote":[105,158],"relatives.":[106],"This":[107],"lower":[108,151],"accuracy":[110],"cannot":[111],"improved":[113],"when":[114],"most":[116,213],"members":[118,135],"are":[122],"excluded":[123],"profiles.":[126],"On":[127],"contrary,":[129],"presence":[131],"results":[136,185],"For":[141],"high":[145],"homologs,":[149],"relatives":[159],"seems":[160],"attribute":[164],"or":[168],"alignments,":[170],"rather":[171],"than":[172],"caused":[175],"large":[178],"sequences":[182],"itself.":[183],"Our":[184],"suggest":[186],"at":[188],"any":[189],"level":[190],"diversity,":[193],"one":[194],"should":[195],"include":[196],"as":[201,206],"many":[202],"possible":[207],"order":[209],"results.":[215]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
