{"id":"https://openalex.org/W2102677343","doi":"https://doi.org/10.1093/nar/gkg504","title":"ORFeus: detection of distant homology using sequence profiles and predicted secondary structure","display_name":"ORFeus: detection of distant homology using sequence profiles and predicted secondary structure","publication_year":2003,"publication_date":"2003-06-25","ids":{"openalex":"https://openalex.org/W2102677343","doi":"https://doi.org/10.1093/nar/gkg504","mag":"2102677343","pmid":"https://pubmed.ncbi.nlm.nih.gov/12824423"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg504","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3804/9487084/gkg504.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","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/nar/article-pdf/31/13/3804/9487084/gkg504.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044789608","display_name":"Krzysztof Ginalski","orcid":"https://orcid.org/0000-0001-7538-1571"},"institutions":[{"id":"https://openalex.org/I4210132495","display_name":"BioInfoBank Institute","ror":"https://ror.org/0432q4w56","country_code":"PL","type":"nonprofit","lineage":["https://openalex.org/I4210132495"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"K. Ginalski","raw_affiliation_strings":["Bioinformatics Laboratory, BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Laboratory, BioInfoBank Institute, ul. Limanowskiego 24A, 60-744 Poznan, Poland","institution_ids":["https://openalex.org/I4210132495"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044789608"],"corresponding_institution_ids":["https://openalex.org/I4210132495"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":5.7265,"has_fulltext":false,"cited_by_count":130,"citation_normalized_percentile":{"value":0.97011338,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"31","issue":"13","first_page":"3804","last_page":"3807"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T11162","display_name":"Enzyme Structure and Function","score":0.9983000159263611,"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/biology","display_name":"Biology","score":0.8626177906990051},{"id":"https://openalex.org/keywords/sequence-homology","display_name":"Sequence homology","score":0.7293392419815063},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.6820691227912903},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6127881407737732},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.6116952896118164},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5830760598182678},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.44521433115005493},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4316794276237488},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.421281635761261},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.4173591434955597},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4108950197696686},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3870677351951599},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3292596638202667},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2399202287197113},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15730935335159302},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.13757669925689697},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.12777003645896912},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.11248466372489929},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09940820932388306}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8626177906990051},{"id":"https://openalex.org/C2779315201","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Sequence homology","level":4,"score":0.7293392419815063},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.6820691227912903},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6127881407737732},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.6116952896118164},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5830760598182678},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.44521433115005493},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4316794276237488},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.421281635761261},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.4173591434955597},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4108950197696686},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3870677351951599},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3292596638202667},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2399202287197113},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15730935335159302},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.13757669925689697},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.12777003645896912},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.11248466372489929},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09940820932388306},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkg504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg504","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3804/9487084/gkg504.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12824423","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12824423","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.547.8666","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.547.8666","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/31/13/3804.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:158790","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC168911","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168911","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:168911","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/168911","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkg504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg504","pdf_url":"https://academic.oup.com/nar/article-pdf/31/13/3804/9487084/gkg504.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.699999988079071}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1969995117","https://openalex.org/W1971596502","https://openalex.org/W2004228538","https://openalex.org/W2011769393","https://openalex.org/W2062123114","https://openalex.org/W2084466582","https://openalex.org/W2094051420","https://openalex.org/W2099075703","https://openalex.org/W2117077088","https://openalex.org/W2133312664","https://openalex.org/W2144483796","https://openalex.org/W2147667050","https://openalex.org/W2151631782","https://openalex.org/W2153187042","https://openalex.org/W2158714788","https://openalex.org/W2169213029","https://openalex.org/W2170962128","https://openalex.org/W2916657753","https://openalex.org/W4235848672"],"related_works":["https://openalex.org/W24291664","https://openalex.org/W1989090710","https://openalex.org/W1741740882","https://openalex.org/W1525517788","https://openalex.org/W2005647400","https://openalex.org/W2571662673","https://openalex.org/W3119443523","https://openalex.org/W4288077714","https://openalex.org/W2516038502","https://openalex.org/W4386496033"],"abstract_inverted_index":{"ORFeus":[0,29],"is":[1,73,100,130],"a":[2,57,88,92,119,122],"fully":[3],"automated,":[4],"sensitive":[5,102],"protein":[6,41,108],"sequence":[7,53,79,90],"similarity":[8],"search":[9],"server":[10],"available":[11],"to":[12,31,49],"the":[13,17,26,33,36,50,67,83,95,127,133,139],"academic":[14],"community":[15],"via":[16],"Structure":[18],"Prediction":[19],"Meta":[20],"Server":[21],"(http://BioInfo.PL/Meta/).":[22],"The":[23,64,124],"goal":[24],"of":[25,28,35,38,66,86,97,126],"development":[27],"was":[30,47],"increase":[32],"sensitivity":[34],"detection":[37],"distantly":[39],"related":[40],"families.":[42],"Predicted":[43],"secondary":[44],"structure":[45],"information":[46,51,80],"added":[48],"about":[52],"conservation":[54],"and":[55,81],"variability,":[56],"technique":[58],"known":[59],"from":[60],"hybrid":[61],"threading":[62],"approaches.":[63],"accuracy":[65],"meta":[68,98],"profiles":[69,76,99,115],"created":[70],"this":[71],"way":[72],"compared":[74,137],"with":[75,82,91,121,138],"containing":[77],"only":[78],"standard":[84],"approach":[85],"aligning":[87,112,118],"single":[89],"profile.":[93],"Additionally,":[94],"alignment":[96,128],"more":[101],"in":[103,132],"detecting":[104],"remote":[105],"homology":[106],"between":[107],"families":[109],"than":[110],"if":[111,117],"two":[113],"sequence-only":[114,141],"or":[116],"profile":[120],"sequence.":[123],"specificity":[125,135],"score":[129],"improved":[131],"lower":[134],"range":[136],"robust":[140],"profiles.":[142]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-19T21:40:30.786675","created_date":"2025-10-10T00:00:00"}
