{"id":"https://openalex.org/W2119699021","doi":"https://doi.org/10.1093/nar/gki424","title":"Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles","display_name":"Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles","publication_year":2005,"publication_date":"2005-06-26","ids":{"openalex":"https://openalex.org/W2119699021","doi":"https://doi.org/10.1093/nar/gki424","mag":"2119699021","pmid":"https://pubmed.ncbi.nlm.nih.gov/15980539"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki424","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W573/7623067/gki424.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/33/suppl_2/W573/7623067/gki424.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060717831","display_name":"Eivind T\u00f8stesen","orcid":"https://orcid.org/0000-0002-5856-6416"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"E. Tostesen","raw_affiliation_strings":["University of Oslo#TAB#"],"affiliations":[{"raw_affiliation_string":"University of Oslo#TAB#","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057128874","display_name":"Geir Ivar Jerstad","orcid":null},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"G. I. Jerstad","raw_affiliation_strings":["Department of Informatics, University of Oslo, N-0316 Oslo, Norway","University of Oslo#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Oslo, N-0316 Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"University of Oslo#TAB#","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083493986","display_name":"Eivind Hovig","orcid":"https://orcid.org/0000-0002-9103-1077"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E. Hovig","raw_affiliation_strings":["Institute for Cancer Research"],"affiliations":[{"raw_affiliation_string":"Institute for Cancer Research","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060717831"],"corresponding_institution_ids":["https://openalex.org/I184942183"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.0066,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.74370284,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"Web Server","first_page":"W573","last_page":"W576"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","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/T10432","display_name":"DNA and Nucleic Acid Chemistry","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980999827384949,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9980000257492065,"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/biology","display_name":"Biology","score":0.801186203956604},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6021484136581421},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5942608714103699},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4925718903541565},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4478045701980591},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.29532697796821594},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.239904522895813},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23931166529655457}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.801186203956604},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6021484136581421},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5942608714103699},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4925718903541565},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4478045701980591},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.29532697796821594},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.239904522895813},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23931166529655457}],"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009691","descriptor_name":"Nucleic Acid Denaturation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009691","descriptor_name":"Nucleic Acid Denaturation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009691","descriptor_name":"Nucleic Acid Denaturation","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":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gki424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki424","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W573/7623067/gki424.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15980539","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15980539","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:155205","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160185","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"}],"best_oa_location":{"id":"doi:10.1093/nar/gki424","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki424","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W573/7623067/gki424.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2119699021.pdf","grobid_xml":"https://content.openalex.org/works/W2119699021.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W176261813","https://openalex.org/W1576596365","https://openalex.org/W1968860042","https://openalex.org/W1989162094","https://openalex.org/W1996259602","https://openalex.org/W2012210882","https://openalex.org/W2017147864","https://openalex.org/W2042282283","https://openalex.org/W2054115419","https://openalex.org/W2070484449","https://openalex.org/W2077740252","https://openalex.org/W2088306370","https://openalex.org/W2097632362","https://openalex.org/W2103123883","https://openalex.org/W2119447107","https://openalex.org/W2135995702","https://openalex.org/W2149722803","https://openalex.org/W2149917234","https://openalex.org/W2168393276"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"In":[0],"this":[1],"study,":[2],"we":[3],"describe":[4],"a":[5,58,76],"web":[6],"server":[7],"that":[8,49],"performs":[9],"computations":[10],"on":[11],"DNA":[12,50],"melting,":[13],"thus":[14],"predicting":[15],"the":[16,20,27,44,62],"localized":[17],"separation":[18],"of":[19,46,68,88],"two":[21],"strands":[22],"for":[23],"sequences":[24],"provided":[25],"by":[26],"users.":[28],"The":[29,94],"output":[30],"types":[31],"are":[32,96],"stitch":[33,59],"profiles,":[34,38],"melting":[35],"curves,":[36],"probability":[37],"etc.":[39],"Stitch":[40],"profile":[41,60],"diagrams":[42],"visualize":[43],"ensemble":[45],"alternative":[47],"conformations":[48],"can":[51,91],"adopt":[52],"with":[53,80],"different":[54],"probabilities.":[55],"For":[56],"example,":[57],"shows":[61],"possible":[63],"loop":[64],"openings":[65],"in":[66],"terms":[67],"their":[69],"locations,":[70],"sizes,":[71],"probabilities":[72],"and":[73],"fluctuations":[74],"at":[75,99],"given":[77],"temperature.":[78],"Sequences":[79],"lengths":[81],"up":[82],"to":[83],"several":[84],"tens":[85],"or":[86],"hundreds":[87],"kilobase":[89],"pairs":[90],"be":[92],"analysed.":[93],"tools":[95],"freely":[97],"available":[98],"http://stitchprofiles.uio.no.":[100]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2016-06-24T00:00:00"}
