{"id":"https://openalex.org/W2087364177","doi":"https://doi.org/10.1093/nar/gkj159","title":"Transterm--extended search facilities and improved integration with other databases","display_name":"Transterm--extended search facilities and improved integration with other databases","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W2087364177","doi":"https://doi.org/10.1093/nar/gkj159","mag":"2087364177","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381889"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj159","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj159","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D37/3926597/gkj159.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":true,"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":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D37/3926597/gkj159.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070093363","display_name":"Grant Jacobs","orcid":null},"institutions":[{"id":"https://openalex.org/I80281795","display_name":"University of Otago","ror":"https://ror.org/01jmxt844","country_code":"NZ","type":"education","lineage":["https://openalex.org/I80281795"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"G. H. Jacobs","raw_affiliation_strings":["Department of Biochemistry and Centre for Gene Research, University of Otago, PO Box 56, Dunedin, New Zealand","Department of Biochemistry and Centre for Gene Research University of Otago PO Box 56 Dunedin New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Centre for Gene Research, University of Otago, PO Box 56, Dunedin, New Zealand","institution_ids":["https://openalex.org/I80281795"]},{"raw_affiliation_string":"Department of Biochemistry and Centre for Gene Research University of Otago PO Box 56 Dunedin New Zealand","institution_ids":["https://openalex.org/I80281795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5070093363"],"corresponding_institution_ids":["https://openalex.org/I80281795"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.8996,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.84885698,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"34","issue":"90001","first_page":"D37","last_page":"D40"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9995999932289124,"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":0.9995999932289124,"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/T11482","display_name":"RNA modifications and cancer","score":0.9995999932289124,"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/T10604","display_name":"RNA Research and Splicing","score":0.9994000196456909,"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/refseq","display_name":"RefSeq","score":0.9272019863128662},{"id":"https://openalex.org/keywords/genbank","display_name":"GenBank","score":0.7642406225204468},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6222326755523682},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.5420511364936829},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5206350684165955},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.4974038898944855},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4427468478679657},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.440265953540802},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4016869068145752},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3434514105319977},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3369326889514923},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3293952941894531},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15476244688034058},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10414448380470276},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.10273745656013489}],"concepts":[{"id":"https://openalex.org/C151810110","wikidata":"https://www.wikidata.org/wiki/Q7307074","display_name":"RefSeq","level":4,"score":0.9272019863128662},{"id":"https://openalex.org/C79029880","wikidata":"https://www.wikidata.org/wiki/Q901755","display_name":"GenBank","level":3,"score":0.7642406225204468},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6222326755523682},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.5420511364936829},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5206350684165955},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.4974038898944855},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4427468478679657},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.440265953540802},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4016869068145752},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3434514105319977},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3369326889514923},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3293952941894531},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15476244688034058},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10414448380470276},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.10273745656013489},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038621","descriptor_name":"Regulatory Sequences, Ribonucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkj159","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj159","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D37/3926597/gkj159.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":true,"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:16381889","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381889","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:europepmc.org:156941","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1347521","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:1347521","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347521","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/gkj159","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj159","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D37/3926597/gkj159.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":true,"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","score":0.5799999833106995,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334749","display_name":"Health Research Council of New Zealand","ror":"https://ror.org/00zbf3d93"},{"id":"https://openalex.org/F4320335369","display_name":"Marsden Fund","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1979098238","https://openalex.org/W2018548355","https://openalex.org/W2022846180","https://openalex.org/W2024177760","https://openalex.org/W2059938159","https://openalex.org/W2062862623","https://openalex.org/W2092006839","https://openalex.org/W2100537111","https://openalex.org/W2128905448","https://openalex.org/W2158381555","https://openalex.org/W2158714788","https://openalex.org/W2162563495","https://openalex.org/W2342044710","https://openalex.org/W4230981326","https://openalex.org/W4246395620","https://openalex.org/W4256438495"],"related_works":["https://openalex.org/W2990171052","https://openalex.org/W3028206028","https://openalex.org/W3206675662","https://openalex.org/W3028050938","https://openalex.org/W2124685016","https://openalex.org/W4229706141","https://openalex.org/W2150215096","https://openalex.org/W4386774076","https://openalex.org/W2415364668","https://openalex.org/W4230992309"],"abstract_inverted_index":{"Transterm":[0,172],"has":[1],"now":[2,112],"been":[3,12],"publicly":[4],"available":[5],"for":[6,29,80,100,127,149],">10":[7],"years.":[8],"Major":[9],"changes":[10],"have":[11],"made":[13],"since":[14],"its":[15],"last":[16],"description":[17],"in":[18,22,117],"this":[19,153],"database":[20,26,37,58,89,110,141],"issue":[21],"2002.":[23],"The":[24,54,88,140,176],"current":[25],"provides":[27],"data":[28,170],"key":[30,55],"regions":[31,57],"of":[32,38,137],"mRNA":[33,39,52,56],"sequences,":[34,133],"a":[35],"curated":[36],"motifs":[40,50,128,144],"and":[41,67,73,77,86,95,134,158],"tools":[42],"to":[43,46,97,119,125],"allow":[44],"users":[45,124],"investigate":[47],"their":[48,168],"own":[49],"or":[51,145,173],"sequences.":[53],"is":[59,90,178],"derived":[60],"computationally":[61],"from":[62,84,156],"Genbank.":[63],"It":[64],"contains":[65,142],"3'":[66],"5'":[68],"flanking":[69],"regions,":[70],"the":[71,109,135],"initiation":[72],"termination":[74],"signal":[75],"context":[76],"coding":[78],"sequence":[79,169],"annotated":[81],"CDS":[82],"features":[83],"Genbank":[85],"RefSeq.":[87],"non-redundant,":[91],"enabling":[92],"summary":[93],"files":[94],"statistics":[96],"be":[98,113],"prepared":[99],"each":[101],"species.":[102],"Advances":[103],"include":[104],"providing":[105],"extended":[106],"search":[107,126,167],"facilities,":[108],"may":[111,166],"searched":[114],"by":[115],"BLAST":[116],"addition":[118],"regular":[120],"expressions":[121],"(patterns)":[122],"allowing":[123],"such":[129],"as":[130],"known":[131],"miRNA":[132],"inclusion":[136],"RefSeq":[138],"data.":[139],">40":[143],"structural":[146],"patterns":[147,155],"important":[148],"translational":[150],"control.":[151],"In":[152],"release,":[154],"UTRsite":[157],"Rfam":[159],"are":[160],"also":[161],"incorporated":[162],"with":[163,171],"cross-referencing.":[164],"Users":[165],"user-defined":[174],"patterns.":[175],"system":[177],"accessible":[179],"at":[180],"http://uther.otago.ac.nz/Transterm.html.":[181]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
