{"id":"https://openalex.org/W3003196708","doi":"https://doi.org/10.1093/bioinformatics/btaa065","title":"LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins","display_name":"LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins","publication_year":2020,"publication_date":"2020-01-23","ids":{"openalex":"https://openalex.org/W3003196708","doi":"https://doi.org/10.1093/bioinformatics/btaa065","mag":"3003196708","pmid":"https://pubmed.ncbi.nlm.nih.gov/32003788"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa065","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa065","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2731/33180998/btaa065.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2731/33180998/btaa065.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029867152","display_name":"Anastasia Gulyaeva","orcid":"https://orcid.org/0000-0002-3587-3587"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Anastasia A Gulyaeva","raw_affiliation_strings":["Department of Medical Microbiology , Leiden University Medical Center, Leiden 2300 RC, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Microbiology , Leiden University Medical Center, Leiden 2300 RC, The Netherlands","institution_ids":["https://openalex.org/I2800006345"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000630149","display_name":"Andrey I Sigorskih","orcid":null},"institutions":[{"id":"https://openalex.org/I4210145583","display_name":"Bioengineering Center","ror":"https://ror.org/04f0ydx59","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210145583"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrey I Sigorskih","raw_affiliation_strings":["Faculty of Bioengineering and Bioinformatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Bioengineering and Bioinformatics","institution_ids":["https://openalex.org/I4210145583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074233644","display_name":"Elena S Ocheredko","orcid":null},"institutions":[{"id":"https://openalex.org/I4210145583","display_name":"Bioengineering Center","ror":"https://ror.org/04f0ydx59","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210145583"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Elena S Ocheredko","raw_affiliation_strings":["Faculty of Bioengineering and Bioinformatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Bioengineering and Bioinformatics","institution_ids":["https://openalex.org/I4210145583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039668629","display_name":"Dmitry V. Samborskiy","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Dmitry V Samborskiy","raw_affiliation_strings":["Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University, Moscow 119899, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University, Moscow 119899, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038215233","display_name":"Alexander E. Gorbalenya","orcid":"https://orcid.org/0000-0002-4967-7341"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I4210145583","display_name":"Bioengineering Center","ror":"https://ror.org/04f0ydx59","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210145583"]}],"countries":["NL","RU"],"is_corresponding":true,"raw_author_name":"Alexander E Gorbalenya","raw_affiliation_strings":["Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University, Moscow 119899, Russia","Department of Biomedical Data Sciences , Leiden University Medical Center, Leiden 2300 RC, The Netherlands","Department of Medical Microbiology , Leiden University Medical Center, Leiden 2300 RC, The Netherlands","Faculty of Bioengineering and Bioinformatics"],"raw_orcid":"https://orcid.org/0000-0002-4967-7341","affiliations":[{"raw_affiliation_string":"Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University, Moscow 119899, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Department of Biomedical Data Sciences , Leiden University Medical Center, Leiden 2300 RC, The Netherlands","institution_ids":["https://openalex.org/I2800006345"]},{"raw_affiliation_string":"Department of Medical Microbiology , Leiden University Medical Center, Leiden 2300 RC, The Netherlands","institution_ids":["https://openalex.org/I2800006345"]},{"raw_affiliation_string":"Faculty of Bioengineering and Bioinformatics","institution_ids":["https://openalex.org/I4210145583"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038215233"],"corresponding_institution_ids":["https://openalex.org/I19880235","https://openalex.org/I2800006345","https://openalex.org/I4210145583"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5221,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.59958782,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"36","issue":"9","first_page":"2731","last_page":"2739"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.2935999929904938,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.2935999929904938,"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":0.28949999809265137,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.09809999912977219,"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/polyproteins","display_name":"Polyproteins","score":0.9620912075042725},{"id":"https://openalex.org/keywords/refseq","display_name":"RefSeq","score":0.7379047274589539},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5713459849357605},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.558508038520813},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5460399389266968},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5096104145050049},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4654432535171509},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4411023259162903},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.42588990926742554},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.37691381573677063},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34170928597450256},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2866945266723633},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22231638431549072},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.21474161744117737},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.200914204120636},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1891154944896698}],"concepts":[{"id":"https://openalex.org/C2910895815","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Polyproteins","level":4,"score":0.9620912075042725},{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.7379047274589539},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5713459849357605},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.558508038520813},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5460399389266968},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5096104145050049},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4654432535171509},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4411023259162903},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.42588990926742554},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.37691381573677063},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34170928597450256},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2866945266723633},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22231638431549072},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.21474161744117737},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.200914204120636},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1891154944896698},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"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":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012328","descriptor_name":"RNA Viruses","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020815","descriptor_name":"Polyproteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020815","descriptor_name":"Polyproteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020815","descriptor_name":"Polyproteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaa065","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa065","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2731/33180998/btaa065.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32003788","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32003788","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:lumc:oai:scholarlypublications.universiteitleiden.nl:item_3181262","is_oa":true,"landing_page_url":"http://hdl.handle.net/1887/3181262","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 36(9), 2731 - 2739. OXFORD UNIV PRESS","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7203729","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7203729","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3181262","is_oa":true,"landing_page_url":"https://academic.oup.com/bioinformatics/article/36/9/2731/5719022","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Article / Letter to editor"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa065","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa065","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/9/2731/33180998/btaa065.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/17","display_name":"Partnerships for the goals","score":0.41999998688697815}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320929","display_name":"Universiteit Leiden","ror":"https://ror.org/027bh9e22"},{"id":"https://openalex.org/F4320323080","display_name":"Leids Universitair Medisch Centrum","ror":"https://ror.org/05xvt9f17"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3003196708.pdf","grobid_xml":"https://content.openalex.org/works/W3003196708.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1552724685","https://openalex.org/W1878730940","https://openalex.org/W1959734218","https://openalex.org/W1980892321","https://openalex.org/W2010061854","https://openalex.org/W2016960645","https://openalex.org/W2027637974","https://openalex.org/W2037684000","https://openalex.org/W2051210555","https://openalex.org/W2064699864","https://openalex.org/W2084247958","https://openalex.org/W2108301842","https://openalex.org/W2108982334","https://openalex.org/W2110650347","https://openalex.org/W2114083522","https://openalex.org/W2114938008","https://openalex.org/W2116160060","https://openalex.org/W2117486996","https://openalex.org/W2125233222","https://openalex.org/W2131478115","https://openalex.org/W2135621733","https://openalex.org/W2141838466","https://openalex.org/W2141885858","https://openalex.org/W2141925828","https://openalex.org/W2145268834","https://openalex.org/W2145605402","https://openalex.org/W2153187042","https://openalex.org/W2158714788","https://openalex.org/W2161072217","https://openalex.org/W2173732482","https://openalex.org/W2243973145","https://openalex.org/W2516022550","https://openalex.org/W2521372695","https://openalex.org/W2522071276","https://openalex.org/W2557595285","https://openalex.org/W2898402099","https://openalex.org/W2945442113","https://openalex.org/W2950954328","https://openalex.org/W2952739713","https://openalex.org/W2972411752","https://openalex.org/W4236459334","https://openalex.org/W4285719527","https://openalex.org/W6677611723"],"related_works":["https://openalex.org/W2066753372","https://openalex.org/W2173732482","https://openalex.org/W2054728806","https://openalex.org/W2167922509","https://openalex.org/W272471359","https://openalex.org/W4388652965","https://openalex.org/W2107903949","https://openalex.org/W3003196708","https://openalex.org/W2941035732","https://openalex.org/W4234194328"],"abstract_inverted_index":{"MOTIVATION:":[0],"To":[1],"facilitate":[2],"accurate":[3],"estimation":[4],"of":[5,8,31,55,81,84,91,109,126,134,153,162,177,182,205,218,232],"statistical":[6,56,89,221],"significance":[7,90,222],"sequence":[9],"similarity":[10,93,226],"in":[11,175,235],"profile-profile":[12],"searches,":[13],"queries":[14,27,44,97,148],"should":[15],"ideally":[16],"correspond":[17],"to":[18,52,167,191],"protein":[19],"domains.":[20],"For":[21],"multidomain":[22,85,122],"proteins,":[23],"using":[24,94,144],"domains":[25],"as":[26,43,147],"depends":[28],"on":[29,216],"delineation":[30],"domain":[32],"borders,":[33],"which":[34,131],"may":[35],"be":[36],"unknown.":[37],"Thus,":[38],"proteins":[39,86,123],"are":[40,254],"commonly":[41],"used":[42,116],"that":[45,73],"complicate":[46],"establishing":[47],"homology":[48],"for":[49,107,119,203,223],"similarities":[50],"close":[51],"cutoff":[53],"levels":[54],"significance.":[57],"RESULTS:":[58],"In":[59],"this":[60],"article,":[61],"we":[62],"describe":[63],"an":[64],"iterative":[65],"approach,":[66],"called":[67],"LAMPA,":[68],"LArge":[69],"Multidomain":[70],"Protein":[71],"Annotator,":[72],"resolves":[74],"the":[75,212],"above":[76],"conundrum":[77],"by":[78,149,156,186,195],"gradual":[79],"expansion":[80],"hit":[82,92,163,220],"coverage":[83,155],"through":[87],"re-evaluating":[88],"ever":[95],"smaller":[96],"defined":[98],"at":[99,247,256],"each":[100],"iteration.":[101],"LAMPA":[102,140,169,187,241],"employs":[103],"TMHMM":[104],"and":[105,112,154,160,200,230],"HHsearch":[106,219],"recognition":[108],"transmembrane":[110],"regions":[111,174],"homology,":[113],"respectively.":[114],"We":[115,210],"Pfam":[117,164],"database":[118],"annotating":[120],"2985":[121],"(polyproteins)":[124],"composed":[125],">1000":[127],"amino":[128],"acid":[129],"residues,":[130],"dominate":[132],"proteomes":[133],"RNA":[135,183,206],"viruses.":[136],"Under":[137],"strict":[138],"cutoffs,":[139],"outperformed":[141],"HHsearch-mediated":[142],"runs":[143],"intact":[145],"polyproteins":[146,185],"three":[150],"measures:":[151],"number":[152,161,199],"identified":[157,170],"homologous":[158,173],"regions,":[159],"profiles.":[165],"Compared":[166],"HHsearch,":[168],"507":[171],"extra":[172],"14.4%":[176],"polyproteins.":[178],"This":[179],"Pfam-based":[180],"annotation":[181,194],"virus":[184,207],"was":[188],"also":[189],"superior":[190],"RefSeq":[192],"expert":[193],"two":[196],"measures,":[197],"region":[198],"annotated":[201],"length,":[202],"69.3%":[204],"polyprotein":[208],"entries.":[209],"rationalized":[211],"obtained":[213],"results":[214],"based":[215],"dependencies":[217],"local":[224],"alignment":[225],"score":[227],"from":[228],"lengths":[229],"diversities":[231],"query-target":[233],"pairs":[234],"computational":[236],"experiments.":[237],"AVAILABILITY":[238],"AND":[239],"IMPLEMENTATION:":[240],"1.0.0":[242],"R":[243],"package":[244],"is":[245],"placed":[246],"github":[248],"(https://github.com/Gorbalenya-Lab/LAMPA).":[249],"SUPPLEMENTARY":[250],"INFORMATION:":[251],"Supplementary":[252],"data":[253],"available":[255],"Bioinformatics":[257],"online.":[258]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
