{"id":"https://openalex.org/W2176355994","doi":"https://doi.org/10.1093/bioinformatics/btv640","title":"Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences","display_name":"Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences","publication_year":2015,"publication_date":"2015-10-30","ids":{"openalex":"https://openalex.org/W2176355994","doi":"https://doi.org/10.1093/bioinformatics/btv640","mag":"2176355994","pmid":"https://pubmed.ncbi.nlm.nih.gov/26519506"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/776/25588872/btv640.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/776/25588872/btv640.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062476988","display_name":"Sumit Mukherjee","orcid":"https://orcid.org/0000-0001-9807-7994"},"institutions":[{"id":"https://openalex.org/I127439422","display_name":"Indian Institute of Science Education and Research Kolkata","ror":"https://ror.org/00djv2c17","country_code":"IN","type":"education","lineage":["https://openalex.org/I127439422"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Sumit Mukherjee","raw_affiliation_strings":["Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India","institution_ids":["https://openalex.org/I127439422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045018479","display_name":"Supratim Sengupta","orcid":"https://orcid.org/0000-0001-5294-0561"},"institutions":[{"id":"https://openalex.org/I127439422","display_name":"Indian Institute of Science Education and Research Kolkata","ror":"https://ror.org/00djv2c17","country_code":"IN","type":"education","lineage":["https://openalex.org/I127439422"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Supratim Sengupta","raw_affiliation_strings":["Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India","institution_ids":["https://openalex.org/I127439422"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062476988"],"corresponding_institution_ids":["https://openalex.org/I127439422"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.108,"has_fulltext":false,"cited_by_count":59,"citation_normalized_percentile":{"value":0.87438488,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"32","issue":"5","first_page":"776","last_page":"778"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.991100013256073,"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":0.991100013256073,"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":0.006200000178068876,"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":0.0006000000284984708,"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/computer-science","display_name":"Computer science","score":0.6006475687026978},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5195937156677246},{"id":"https://openalex.org/keywords/riboswitch","display_name":"Riboswitch","score":0.4921938478946686},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4379361867904663},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36812371015548706},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3254010081291199},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2805284261703491},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19466441869735718},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.11862519383430481}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6006475687026978},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5195937156677246},{"id":"https://openalex.org/C148625055","wikidata":"https://www.wikidata.org/wiki/Q418840","display_name":"Riboswitch","level":5,"score":0.4921938478946686},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4379361867904663},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36812371015548706},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3254010081291199},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2805284261703491},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19466441869735718},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.11862519383430481},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.0}],"mesh":[{"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":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/776/25588872/btv640.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26519506","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26519506","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:oai:open-archive.highwire.org:bioinfo:32/5/776","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/5/776","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv640","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv640","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/776/25588872/btv640.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1669241002","https://openalex.org/W1946428967","https://openalex.org/W1972708527","https://openalex.org/W1981274796","https://openalex.org/W2012879790","https://openalex.org/W2025010701","https://openalex.org/W2055779184","https://openalex.org/W2061930808","https://openalex.org/W2086561953","https://openalex.org/W2096647099","https://openalex.org/W2099628841","https://openalex.org/W2108230379","https://openalex.org/W2119582819","https://openalex.org/W2121918723","https://openalex.org/W2138122982","https://openalex.org/W2141152740","https://openalex.org/W2151831732","https://openalex.org/W2166409098","https://openalex.org/W6656698018"],"related_works":["https://openalex.org/W1507571087","https://openalex.org/W2756374846","https://openalex.org/W2083416401","https://openalex.org/W1982316634","https://openalex.org/W2769114003","https://openalex.org/W21023364","https://openalex.org/W2150147498","https://openalex.org/W2033914206","https://openalex.org/W2009055497","https://openalex.org/W2042327336"],"abstract_inverted_index":{"UNLABELLED:":[0],"Riboswitches":[1],"are":[2,104],"non-coding":[3],"RNA":[4],"located":[5],"in":[6,45,70],"the":[7,20,25,35,46,94],"5'":[8],"untranslated":[9],"regions":[10],"where":[11],"they":[12],"bind":[13],"a":[14,53],"target":[15],"metabolite":[16],"used":[17],"to":[18],"specify":[19],"riboswitch":[21],"class":[22],"and":[23,42,82],"control":[24],"expression":[26],"of":[27,32,68],"associated":[28],"genes.":[29],"Accurate":[30],"identification":[31],"riboswitches":[33,69],"is":[34],"first":[36],"step":[37],"towards":[38],"understanding":[39],"their":[40],"regulatory":[41],"functional":[43],"roles":[44],"cell.":[47],"In":[48],"this":[49],"article,":[50],"we":[51],"describe":[52],"new":[54],"web":[55,95],"application":[56],"named":[57],"Riboswitch":[58,87],"Scanner":[59,88],"which":[60],"provides":[61],"an":[62],"automated":[63],"pipeline":[64],"for":[65],"pHMM-based":[66],"detection":[67],"partial":[71],"as":[72,74],"well":[73],"complete":[75],"genomic":[76],"sequences":[77],"rapidly,":[78],"with":[79],"high":[80],"sensitivity":[81],"specificity.":[83],"AVAILABILITY":[84],"AND":[85],"IMPLEMENTATION:":[86],"can":[89],"be":[90],"freely":[91],"accessed":[92],"on":[93],"at":[96,106],"http://service.iiserkol.ac.in/\u223criboscan/":[97],"CONTACT:":[98],"mukherjee.sumit89@gmail.com":[99],"SUPPLEMENTARY":[100],"INFORMATION:":[101],"Supplementary":[102],"data":[103],"available":[105],"Bioinformatics":[107],"online.":[108]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
