{"id":"https://openalex.org/W1997110152","doi":"https://doi.org/10.1186/1471-2105-12-275","title":"AlignHUSH: Alignment of HMMs using structure and hydrophobicity information","display_name":"AlignHUSH: Alignment of HMMs using structure and hydrophobicity information","publication_year":2011,"publication_date":"2011-07-05","ids":{"openalex":"https://openalex.org/W1997110152","doi":"https://doi.org/10.1186/1471-2105-12-275","mag":"1997110152","pmid":"https://pubmed.ncbi.nlm.nih.gov/21729312"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-275","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-275","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-275","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-275","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078260902","display_name":"Krishnadev Oruganty","orcid":"https://orcid.org/0000-0003-0866-6862"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Oruganty Krishnadev","raw_affiliation_strings":["Molecular Biophysics Unit Indian Institute of Science, Bangalore 560012, India","Molecular Biophysics Unit Indian Institute of Science, Bangalore, India","A318, Biochemistry and Molecular Biology Department, Athens, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit Indian Institute of Science, Bangalore 560012, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Molecular Biophysics Unit Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"A318, Biochemistry and Molecular Biology Department, Athens, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076920718","display_name":"Narayanaswamy Srinivasan","orcid":"https://orcid.org/0000-0002-6566-6239"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Narayanaswamy Srinivasan","raw_affiliation_strings":["Molecular Biophysics Unit Indian Institute of Science, Bangalore, 560012, India","Molecular Biophysics Unit Indian Institute of Science, Bangalore, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Biophysics Unit Indian Institute of Science, Bangalore, 560012, India","institution_ids":["https://openalex.org/I59270414"]},{"raw_affiliation_string":"Molecular Biophysics Unit Indian Institute of Science, Bangalore, India","institution_ids":["https://openalex.org/I59270414"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5076920718"],"corresponding_institution_ids":["https://openalex.org/I59270414"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5321,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.64960413,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"1","first_page":"275","last_page":"275"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7818999886512756,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.7818999886512756,"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/T11162","display_name":"Enzyme Structure and Function","score":0.06679999828338623,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.03319999948143959,"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":0.8143709897994995},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6159712076187134},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5920425057411194},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5717432498931885},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5516895651817322},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5515984892845154},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.547825038433075},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5071902275085449},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.4668821692466736},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.43815451860427856},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4229482114315033},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37003886699676514},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23512691259384155},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22920668125152588},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.16189342737197876},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.11332377791404724},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07857832312583923}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.8143709897994995},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6159712076187134},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5920425057411194},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5717432498931885},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5516895651817322},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5515984892845154},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.547825038433075},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5071902275085449},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.4668821692466736},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.43815451860427856},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4229482114315033},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37003886699676514},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23512691259384155},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22920668125152588},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.16189342737197876},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.11332377791404724},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07857832312583923},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"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":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-12-275","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-275","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-275","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21729312","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21729312","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:eprints.iisc.ac.in:39740","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196309","display_name":"NOT FOUND REPOSITORY (Indian Institute of Science Bangalore)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I59270414","host_organization_name":"Indian Institute of Science Bangalore","host_organization_lineage":["https://openalex.org/I59270414"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:a22d030251154281a03a495bf7e96a94","is_oa":true,"landing_page_url":"https://doaj.org/article/a22d030251154281a03a495bf7e96a94","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 275 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2237467","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3228556","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-275","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-275","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-275","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320719","display_name":"Department of Science and Technology, Ministry of Science and Technology, India","ror":"https://ror.org/0101xrq71"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1997110152.pdf","grobid_xml":"https://content.openalex.org/works/W1997110152.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W12704442","https://openalex.org/W1422803820","https://openalex.org/W1513621883","https://openalex.org/W1963523582","https://openalex.org/W1965998064","https://openalex.org/W1971751969","https://openalex.org/W1983558037","https://openalex.org/W1995365949","https://openalex.org/W1996112765","https://openalex.org/W2003852785","https://openalex.org/W2022058405","https://openalex.org/W2024239868","https://openalex.org/W2036149515","https://openalex.org/W2051969447","https://openalex.org/W2062693912","https://openalex.org/W2069458148","https://openalex.org/W2073758233","https://openalex.org/W2084052949","https://openalex.org/W2094519647","https://openalex.org/W2099075703","https://openalex.org/W2102122585","https://openalex.org/W2102856132","https://openalex.org/W2105118494","https://openalex.org/W2106868489","https://openalex.org/W2112269777","https://openalex.org/W2114659440","https://openalex.org/W2115138247","https://openalex.org/W2120772351","https://openalex.org/W2122665495","https://openalex.org/W2128653811","https://openalex.org/W2136570298","https://openalex.org/W2143592941","https://openalex.org/W2143705344","https://openalex.org/W2145268834","https://openalex.org/W2150999244","https://openalex.org/W2151831732","https://openalex.org/W2153187042","https://openalex.org/W2158714788","https://openalex.org/W2164886928","https://openalex.org/W2407774140"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W1985408726","https://openalex.org/W1482324242","https://openalex.org/W2088487249","https://openalex.org/W2187357871","https://openalex.org/W2141411672","https://openalex.org/W1981307089","https://openalex.org/W2468116983"],"abstract_inverted_index":{"BACKGROUND:":[0],"Sensitive":[1],"remote":[2,94],"homology":[3,95,163],"detection":[4],"and":[5,22,58,83,93,121,153,165,192,204],"accurate":[6],"alignments":[7,92,136,146],"especially":[8],"in":[9,50,110,148],"the":[10,51,88,101,116,135,144,154,231],"midnight":[11],"zone":[12],"of":[13,25,39,53,60,66,69,74,90,103,134,202,222,224],"sequence":[14],"similarity":[15],"are":[16,157],"needed":[17],"for":[18,30,162,179],"better":[19,114,197],"function":[20,166],"annotation":[21],"structural":[23,48],"modeling":[24,164],"proteins.":[26],"An":[27],"algorithm,":[28],"AlignHUSH":[29,104,112,139,232],"HMM-HMM":[31,91,118],"alignment":[32,119,151,155,169],"has":[33,79,140,189],"been":[34,81,141,190],"developed":[35,191],"which":[36],"is":[37,84,122,171,193,234],"capable":[38],"recognizing":[40],"distantly":[41],"related":[42],"domain":[43],"families":[44],"The":[45,72,150,168,212],"method":[46,185,214,233],"uses":[47],"information,":[49],"form":[52],"predicted":[54],"secondary":[55],"structure":[56],"probabilities,":[57],"hydrophobicity":[59],"amino":[61],"acids":[62],"to":[63,86,124,159,173,176,186,195,208,220],"align":[64,187],"HMMs":[65,188],"two":[67],"sets":[68],"aligned":[70],"sequences.":[71],"effect":[73],"using":[75,105,138,143],"adjoining":[76],"column(s)":[77],"information":[78],"also":[80],"investigated":[82],"found":[85,158,172],"increase":[87],"sensitivity":[89,198],"detection.":[96],"RESULTS:":[97],"We":[98],"have":[99,196],"assessed":[100,142],"performance":[102],"known":[106],"evolutionary":[107],"relationships":[108],"available":[109,147,210,235],"SCOP.":[111],"performs":[113],"than":[115],"best":[117],"methods":[120,178],"observed":[123],"be":[125,160,174],"even":[126],"more":[127],"sensitive":[128],"at":[129,199,236],"higher":[130],"error":[131,200],"rates.":[132],"Accuracy":[133],"obtained":[137],"structure-based":[145],"BaliBASE.":[149],"length":[152],"quality":[156],"appropriate":[161],"annotation.":[167],"accuracy":[170],"comparable":[175],"existing":[177],"profile-profile":[180],"alignments.":[181],"CONCLUSIONS:":[182],"A":[183,228],"new":[184],"shown":[194],"rates":[201],"10%":[203],"above":[205],"when":[206],"compared":[207],"other":[209],"programs.":[211],"proposed":[213],"could":[215],"effectively":[216],"aid":[217],"obtaining":[218],"clues":[219],"functions":[221],"proteins":[223],"yet":[225],"unknown":[226],"function.":[227],"web-server":[229],"incorporating":[230],"http://crick.mbu.iisc.ernet.in/~alignhush/":[237]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
