{"id":"https://openalex.org/W2020456609","doi":"https://doi.org/10.1093/nar/gkq487","title":"PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences","display_name":"PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences","publication_year":2010,"publication_date":"2010-06-03","ids":{"openalex":"https://openalex.org/W2020456609","doi":"https://doi.org/10.1093/nar/gkq487","mag":"2020456609","pmid":"https://pubmed.ncbi.nlm.nih.gov/20522510"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq487","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W59/3898321/gkq487.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/38/suppl_2/W59/3898321/gkq487.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083638854","display_name":"Satish Chikkagoudar","orcid":"https://orcid.org/0000-0002-4547-3480"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Chikkagoudar","raw_affiliation_strings":["Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA","Department of Biostatistics and Epidemiology University of Pennsylvania School of Medicine Philadelphia Pennsylvania USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Biostatistics and Epidemiology University of Pennsylvania School of Medicine Philadelphia Pennsylvania USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054458396","display_name":"Dennis R. Livesay","orcid":null},"institutions":[{"id":"https://openalex.org/I102149020","display_name":"University of North Carolina at Charlotte","ror":"https://ror.org/04dawnj30","country_code":"US","type":"education","lineage":["https://openalex.org/I102149020"]},{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]},{"id":"https://openalex.org/I922845939","display_name":"Philadelphia University","ror":"https://ror.org/03zzmyz63","country_code":"US","type":"education","lineage":["https://openalex.org/I922845939"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. R. Livesay","raw_affiliation_strings":["Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, 2Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina and 3Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA","University of Pennsylvania, Philadelphia, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, 2Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina and 3Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA","institution_ids":["https://openalex.org/I118118575","https://openalex.org/I102149020","https://openalex.org/I79576946"]},{"raw_affiliation_string":"University of Pennsylvania, Philadelphia, United States","institution_ids":["https://openalex.org/I922845939","https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087990990","display_name":"Usman Roshan","orcid":null},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]},{"id":"https://openalex.org/I922845939","display_name":"Philadelphia University","ror":"https://ror.org/03zzmyz63","country_code":"US","type":"education","lineage":["https://openalex.org/I922845939"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"U. Roshan","raw_affiliation_strings":["University of Pennsylvania, Philadelphia, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pennsylvania, Philadelphia, United States","institution_ids":["https://openalex.org/I922845939","https://openalex.org/I79576946"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.8168,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.71356061,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"38","issue":"Web Server","first_page":"W59","last_page":"W63"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998999834060669,"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":0.9945999979972839,"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":0.7598790526390076},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5979942083358765},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5758614540100098},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.5148386359214783},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5027475357055664},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4493749439716339},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4344833493232727},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4215020537376404},{"id":"https://openalex.org/keywords/posterior-probability","display_name":"Posterior probability","score":0.410361647605896},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3641228675842285},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2945319414138794},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21402329206466675},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18977537751197815},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09112036228179932}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7598790526390076},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5979942083358765},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5758614540100098},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.5148386359214783},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5027475357055664},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4493749439716339},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4344833493232727},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4215020537376404},{"id":"https://openalex.org/C57830394","wikidata":"https://www.wikidata.org/wiki/Q278079","display_name":"Posterior probability","level":3,"score":0.410361647605896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3641228675842285},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2945319414138794},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21402329206466675},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18977537751197815},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09112036228179932},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.0}],"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":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","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":"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkq487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq487","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W59/3898321/gkq487.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:20522510","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20522510","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:10.1.1.354.4263","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.354.4263","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/b9/9d/Nucleic_Acids_Res_2010_Jul_1_38(Web_Server_issue)_W59-W63.tar.gz","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:nar:38/suppl_2/W59","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/38/suppl_2/W59","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:2896107","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2896107","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/gkq487","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq487","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W59/3898321/gkq487.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1977171066","https://openalex.org/W2026210129","https://openalex.org/W2042881722","https://openalex.org/W2055043387","https://openalex.org/W2069394224","https://openalex.org/W2087064593","https://openalex.org/W2103348662","https://openalex.org/W2121691652","https://openalex.org/W2124662626","https://openalex.org/W2139401433","https://openalex.org/W2150504532","https://openalex.org/W4236236547"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2141411672"],"abstract_inverted_index":{"Alignment-based":[0],"programs":[1],"are":[2,38,79],"valuable":[3],"tools":[4],"for":[5],"finding":[6],"potential":[7],"homologs":[8],"in":[9,30,40,90],"genome":[10,70],"sequences.":[11],"Previously,":[12],"it":[13],"has":[14],"been":[15],"shown":[16],"that":[17,37,51,78,108],"partition":[18],"function":[19],"posterior":[20,83,121],"probabilities":[21],"attuned":[22],"to":[23,94],"local":[24,95,125],"alignment":[25,52,105],"achieve":[26],"a":[27,41,63,68,74,81,91,110],"high":[28,120],"accuracy":[29],"identifying":[31],"distantly":[32],"similar":[33],"non-coding":[34],"RNA":[35,65],"sequences":[36],"hidden":[39],"large":[42,69],"genome.":[43],"Here,":[44],"we":[45],"present":[46],"an":[47],"online":[48],"implementation":[49],"of":[50,76,112,119],"algorithm":[53],"based":[54],"on":[55],"such":[56],"probabilities.":[57],"Our":[58],"server":[59,128],"takes":[60],"as":[61],"input":[62],"query":[64],"sequence":[66],"and":[67,72,116],"sequence,":[71],"outputs":[73],"list":[75,111],"hits":[77,114],"above":[80],"mean":[82],"probability":[84,122],"threshold.":[85],"The":[86,127],"output":[87],"is":[88,129],"presented":[89],"format":[92],"suited":[93],"alignment.":[96,126],"It":[97],"can":[98],"also":[99],"be":[100],"viewed":[101],"within":[102,123],"the":[103],"PLAST":[104],"viewer":[106],"applet":[107],"provides":[109],"all":[113],"found":[115],"highlights":[117],"regions":[118],"each":[124],"freely":[130],"available":[131],"at":[132],"http://plastrna.njit.edu.":[133]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
