{"id":"https://openalex.org/W2106739493","doi":"https://doi.org/10.1093/nar/gkh067","title":"trome, trEST and trGEN: databases of predicted protein sequences","display_name":"trome, trEST and trGEN: databases of predicted protein sequences","publication_year":2003,"publication_date":"2003-12-18","ids":{"openalex":"https://openalex.org/W2106739493","doi":"https://doi.org/10.1093/nar/gkh067","mag":"2106739493","pmid":"https://pubmed.ncbi.nlm.nih.gov/14681469"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkh067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh067","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_1/D509/7621616/gkh067.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/32/suppl_1/D509/7621616/gkh067.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041806695","display_name":"Peter Sperisen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"P. Sperisen","raw_affiliation_strings":["Swiss Institute of Bioinformatics, Ludwig Institute for Cancer Research, Chemin des Boveresses 155, 1066 Epalinges s/Lausanne, Switzerland. peter.sperisen@isb-sib.ch","Swiss Institute of Bioinformatics, Ludwig Institute for Cancer Research, Chemin des Boveresses 155, 1066 Epalinges s/Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Ludwig Institute for Cancer Research, Chemin des Boveresses 155, 1066 Epalinges s/Lausanne, Switzerland. peter.sperisen@isb-sib.ch","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210117758"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Ludwig Institute for Cancer Research, Chemin des Boveresses 155, 1066 Epalinges s/Lausanne, Switzerland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041806695"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I4210117758"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":0.7982,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.70204428,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"32","issue":"90001","first_page":"509D","last_page":"511"},"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9970999956130981,"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":0.9948999881744385,"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/database","display_name":"Database","score":0.7632186412811279},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7416061758995056},{"id":"https://openalex.org/keywords/file-transfer-protocol","display_name":"File Transfer Protocol","score":0.6203795075416565},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.42101868987083435},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3229466378688812},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2298068404197693},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.19213151931762695},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.08870819211006165}],"concepts":[{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.7632186412811279},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7416061758995056},{"id":"https://openalex.org/C169485995","wikidata":"https://www.wikidata.org/wiki/Q42283","display_name":"File Transfer Protocol","level":3,"score":0.6203795075416565},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.42101868987083435},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3229466378688812},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2298068404197693},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.19213151931762695},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.08870819211006165},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","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},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1093/nar/gkh067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh067","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_1/D509/7621616/gkh067.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:14681469","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14681469","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:10.1.1.1010.878","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1010.878","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://myhits.isb-sib.ch/doc/pdf/trestNAR04.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1015.4668","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1015.4668","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/32/suppl_1/D509.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:161237","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/308801","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":null,"raw_type":"Text"},{"id":"pmh:oai:infoscience.epfl.ch:114903","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/114903","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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:infoscience.tind.io:114903","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/15736","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"research article"},{"id":"pmh:oai:iris.unil.ch:iris/210074","is_oa":false,"landing_page_url":"https://iris.unil.ch/handle/iris/210074","pdf_url":null,"source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:serval.unil.ch:BIB_BD2F5B01B19E","is_oa":false,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_BD2F5B01B19E","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, vol. 32, no. Database issue, pp. D509-D511","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkh067","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkh067","pdf_url":"https://academic.oup.com/nar/article-pdf/32/suppl_1/D509/7621616/gkh067.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":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320311496","display_name":"Ludwig Institute for Cancer Research","ror":"https://ror.org/05qdwtz81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106739493.pdf","grobid_xml":"https://content.openalex.org/works/W2106739493.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1986891966","https://openalex.org/W2037500862","https://openalex.org/W2044230490","https://openalex.org/W2055247169","https://openalex.org/W2055666215","https://openalex.org/W2058034836","https://openalex.org/W2080667183","https://openalex.org/W2088706346","https://openalex.org/W2110041134","https://openalex.org/W2129303655","https://openalex.org/W2137986897","https://openalex.org/W2156362263","https://openalex.org/W2166359901","https://openalex.org/W2809328794","https://openalex.org/W4232188079","https://openalex.org/W4248523731"],"related_works":["https://openalex.org/W1964593801","https://openalex.org/W2382208609","https://openalex.org/W2061282752","https://openalex.org/W1985300750","https://openalex.org/W3210523558","https://openalex.org/W3210090277","https://openalex.org/W4238583059","https://openalex.org/W1974746088","https://openalex.org/W2098014738","https://openalex.org/W1979071480"],"abstract_inverted_index":{"We":[0],"previously":[1],"introduced":[2],"two":[3,29],"new":[4,33,55,79],"protein":[5,12],"databases":[6,30,80],"(trEST":[7,93],"and":[8,17,51,61,86,94],"trGEN)":[9,95],"of":[10,39,58,74],"hypothetical":[11],"sequences":[13],"predicted":[14],"from":[15,108],"EST":[16,40],"HTG":[18,43],"sequences,":[19],"respectively.":[20],"Here,":[21],"we":[22],"present":[23],"the":[24,65],"updates":[25],"made":[26],"on":[27,89],"these":[28],"plus":[31],"a":[32,68,83,90],"database":[34,56],"(trome),":[35],"which":[36],"uses":[37],"alignments":[38],"data":[41],"to":[42,47],"or":[44,96],"full":[45],"genomes":[46],"generate":[48],"virtual":[49],"transcripts":[50],"coding":[52],"sequences.":[53],"This":[54],"is":[57,73],"higher":[59],"quality":[60],"since":[62],"it":[63,72],"contains":[64],"information":[66],"in":[67,82],"much":[69,75],"denser":[70],"format":[71,85],"smaller":[76],"size.":[77],"These":[78],"are":[81,87],"Swiss-Prot-like":[84],"updated":[88],"weekly":[91],"basis":[92],"every":[97],"3":[98],"months":[99],"(trome).":[100],"They":[101],"can":[102],"be":[103],"downloaded":[104],"by":[105],"anonymous":[106],"ftp":[107],"ftp://ftp.isrec.isb-sib.ch/pub/databases.":[109]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
