{"id":"https://openalex.org/W2170421047","doi":"https://doi.org/10.1186/1471-2105-8-435","title":"Improving model construction of profile HMMs for remote homology detection through structural alignment","display_name":"Improving model construction of profile HMMs for remote homology detection through structural alignment","publication_year":2007,"publication_date":"2007-11-09","ids":{"openalex":"https://openalex.org/W2170421047","doi":"https://doi.org/10.1186/1471-2105-8-435","mag":"2170421047","pmid":"https://pubmed.ncbi.nlm.nih.gov/17999748"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-435","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-435","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-435","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/10.1186/1471-2105-8-435","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089115213","display_name":"Juliana Bernardes","orcid":"https://orcid.org/0000-0003-1341-4256"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Juliana S Bernardes","raw_affiliation_strings":["COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. julibinho@gmail.com","COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. julibinho@gmail.com","institution_ids":["https://openalex.org/I122140584"]},{"raw_affiliation_string":"COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I122140584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024614936","display_name":"Alberto M. R. D\u00e1vila","orcid":"https://orcid.org/0000-0002-6918-7673"},"institutions":[{"id":"https://openalex.org/I52325","display_name":"Funda\u00e7\u00e3o Oswaldo Cruz","ror":"https://ror.org/04jhswv08","country_code":"BR","type":"facility","lineage":["https://openalex.org/I52325"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Alberto MR D\u00e1vila","raw_affiliation_strings":["Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I52325"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059093687","display_name":"V\u0131\u0301tor Santos Costa","orcid":"https://orcid.org/0000-0002-3344-8237"},"institutions":[{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"V\u00edtor S Costa","raw_affiliation_strings":["DCC-FCUP e LIACC, Universidade do Porto, Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DCC-FCUP e LIACC, Universidade do Porto, Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012291023","display_name":"Gerson Zaverucha","orcid":"https://orcid.org/0000-0002-3641-6839"},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Gerson Zaverucha","raw_affiliation_strings":["COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"COPPE, Programa de Engenharia de Sistemas e Computa\u00e7\u00e3o, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I122140584"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5089115213"],"corresponding_institution_ids":["https://openalex.org/I122140584"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.8801,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.72638429,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"1","first_page":"435","last_page":"435"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.40939998626708984,"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":0.40939998626708984,"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":0.1915999948978424,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.15389999747276306,"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":0.7014127373695374},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.6788824796676636},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6675781011581421},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6484422087669373},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.6203370690345764},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45399317145347595},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4387490153312683},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4317964017391205},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.42458999156951904},{"id":"https://openalex.org/keywords/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.4159882962703705},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.41130390763282776},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4110238552093506},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4042779803276062},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3343504071235657},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32332026958465576},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23110681772232056},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1681886911392212},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.12489503622055054}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.7014127373695374},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.6788824796676636},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6675781011581421},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6484422087669373},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.6203370690345764},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45399317145347595},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4387490153312683},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4317964017391205},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.42458999156951904},{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.4159882962703705},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.41130390763282776},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4110238552093506},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4042779803276062},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3343504071235657},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32332026958465576},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23110681772232056},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1681886911392212},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.12489503622055054},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","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":"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":"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":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"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":"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":"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"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":"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":"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:10.1186/1471-2105-8-435","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-435","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-435","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:17999748","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17999748","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:HAL:hal-00684130v1","is_oa":false,"landing_page_url":"https://hal.science/hal-00684130","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, 2007, 8, pp.435. ⟨10.1186/1471-2105-8-435⟩","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:b68d2797bb384503adf12c870d820431","is_oa":true,"landing_page_url":"https://doaj.org/article/b68d2797bb384503adf12c870d820431","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 8, Iss 1, p 435 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1833093","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2245980","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:10.1186/1471-2105-8-435","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-435","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-435","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/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320325035","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170421047.pdf","grobid_xml":"https://content.openalex.org/works/W2170421047.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W11981056","https://openalex.org/W1558365920","https://openalex.org/W1596938234","https://openalex.org/W1775447850","https://openalex.org/W1882120692","https://openalex.org/W1969051510","https://openalex.org/W1969153299","https://openalex.org/W1969621320","https://openalex.org/W1971913854","https://openalex.org/W1975001431","https://openalex.org/W1999569420","https://openalex.org/W2004178884","https://openalex.org/W2004228538","https://openalex.org/W2049821875","https://openalex.org/W2055043387","https://openalex.org/W2058336694","https://openalex.org/W2062296203","https://openalex.org/W2067579500","https://openalex.org/W2082628285","https://openalex.org/W2093534140","https://openalex.org/W2097555181","https://openalex.org/W2097767833","https://openalex.org/W2098464924","https://openalex.org/W2099946731","https://openalex.org/W2101369049","https://openalex.org/W2102122585","https://openalex.org/W2102502076","https://openalex.org/W2104983234","https://openalex.org/W2105118494","https://openalex.org/W2105801262","https://openalex.org/W2106882534","https://openalex.org/W2111373249","https://openalex.org/W2117746967","https://openalex.org/W2120815702","https://openalex.org/W2122665495","https://openalex.org/W2125725297","https://openalex.org/W2125838338","https://openalex.org/W2127122014","https://openalex.org/W2128328428","https://openalex.org/W2130479394","https://openalex.org/W2131889225","https://openalex.org/W2132573698","https://openalex.org/W2140244239","https://openalex.org/W2140455347","https://openalex.org/W2140872496","https://openalex.org/W2141885858","https://openalex.org/W2144319229","https://openalex.org/W2144362290","https://openalex.org/W2145268834","https://openalex.org/W2146086467","https://openalex.org/W2147818576","https://openalex.org/W2147859827","https://openalex.org/W2151831732","https://openalex.org/W2154952425","https://openalex.org/W2158386569","https://openalex.org/W2164886928","https://openalex.org/W2169356867","https://openalex.org/W2477521491","https://openalex.org/W4210400672"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2468116983","https://openalex.org/W2111937814","https://openalex.org/W2029514038","https://openalex.org/W2103737249","https://openalex.org/W2948014085","https://openalex.org/W1486249959","https://openalex.org/W2141411672","https://openalex.org/W1482324242","https://openalex.org/W187239587"],"abstract_inverted_index":{"BACKGROUND:":[0],"Remote":[1],"homology":[2],"detection":[3],"is":[4,167,200],"a":[5,31,211],"challenging":[6],"problem":[7],"in":[8,23,61,90,158,188,218],"Bioinformatics.":[9],"Arguably,":[10],"profile":[11],"Hidden":[12],"Markov":[13],"Models":[14],"(pHMMs)":[15],"are":[16,68,172,181],"one":[17],"of":[18,48,56,86,197,213],"the":[19,46,54,62,84,96,108,177,193],"most":[20],"successful":[21],"approaches":[22],"addressing":[24],"this":[25,166,219],"important":[26,178],"problem.":[27],"pHMM":[28,91],"packages":[29],"present":[30],"relatively":[32],"small":[33],"computational":[34],"cost,":[35],"and":[36,78,110,121,135],"perform":[37,100],"particularly":[38],"well":[39],"at":[40,75,174],"recognizing":[41],"remote":[42],"homologies.":[43],"This":[44],"raises":[45],"question":[47],"whether":[49],"structural":[50,66,88,147,169],"alignments":[51,67,74,89,104,114,148],"could":[52],"impact":[53,85],"performance":[55],"pHMMs":[57,144,153],"trained":[58],"from":[59,146,155],"proteins":[60],"Twilight":[63],"Zone,":[64],"as":[65],"often":[69,183],"more":[70,182],"accurate":[71],"than":[72,152],"sequence":[73,113,156],"identifying":[76],"motifs":[77],"functional":[79],"residues.":[80],"Next,":[81],"we":[82],"assess":[83],"using":[87,107,117],"performance.":[92],"RESULTS:":[93],"We":[94,123,141,164],"used":[95],"SCOP":[97],"database":[98],"to":[99],"our":[101],"experiments.":[102],"Structural":[103],"were":[105,115],"obtained":[106,116],"3DCOFFEE":[109],"MAMMOTH-mult":[111],"tools;":[112],"CLUSTALW,":[118],"TCOFFEE,":[119],"MAFFT":[120],"PROBCONS.":[122],"performed":[124,149],"leave-one-family-out":[125],"cross-validation":[126],"over":[127],"super-families.":[128],"Performance":[129],"was":[130],"evaluated":[131],"through":[132,185],"ROC":[133],"curves":[134],"paired":[136],"two":[137],"tailed":[138],"t-test.":[139],"CONCLUSION:":[140],"observed":[142],"that":[143,180],"derived":[145,154],"significantly":[150],"better":[151,173],"alignment":[157,170],"low-identity":[159,206],"regions,":[160],"mainly":[161],"below":[162],"20%.":[163],"believe":[165],"because":[168],"tools":[171,199],"focusing":[175],"on":[176],"patterns":[179],"conserved":[184],"evolution,":[186],"resulting":[187],"higher":[189],"quality":[190],"pHMMs.":[191],"On":[192],"other":[194],"hand,":[195],"sensitivity":[196],"these":[198,205],"still":[201],"quite":[202],"low":[203],"for":[204,216],"regions.":[207],"Our":[208],"results":[209],"suggest":[210],"number":[212],"possible":[214],"directions":[215],"improvements":[217],"area.":[220]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}