{"id":"https://openalex.org/W2105577015","doi":"https://doi.org/10.1109/ipdps.2004.1303207","title":"Parallel RNA sequence-structure alignment","display_name":"Parallel RNA sequence-structure alignment","publication_year":2004,"publication_date":"2004-06-10","ids":{"openalex":"https://openalex.org/W2105577015","doi":"https://doi.org/10.1109/ipdps.2004.1303207","mag":"2105577015"},"language":"en","primary_location":{"id":"doi:10.1109/ipdps.2004.1303207","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2004.1303207","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"18th International Parallel and Distributed Processing Symposium, 2004. Proceedings.","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100392605","display_name":"Tong Liu","orcid":"https://orcid.org/0000-0001-5497-8117"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Tong Liu","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"B. Schmidt","raw_affiliation_strings":["School of Computer Engineering, Nanyang Technological University, Singapore","Sch. of Comput. Eng., Nanyang Technol. Univ., Singapore#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"Sch. of Comput. Eng., Nanyang Technol. Univ., Singapore#TAB#","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"63","issue":null,"first_page":"190","last_page":"197"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9959999918937683,"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/sequence","display_name":"Sequence (biology)","score":0.680915117263794},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.661038339138031},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6138271689414978},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.5265268087387085},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4981422424316406},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.4801627993583679},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.47946059703826904},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.47286510467529297},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4243493378162384},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3913750648498535},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36424803733825684},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32258328795433044},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2271885871887207},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20871737599372864},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1969079077243805},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.11653134226799011}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.680915117263794},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.661038339138031},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6138271689414978},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.5265268087387085},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4981422424316406},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4801627993583679},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.47946059703826904},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.47286510467529297},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4243493378162384},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3913750648498535},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36424803733825684},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32258328795433044},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2271885871887207},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20871737599372864},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1969079077243805},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.11653134226799011},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/ipdps.2004.1303207","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2004.1303207","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"18th International Parallel and Distributed Processing Symposium, 2004. Proceedings.","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.2.6370","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.2.6370","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.hicomb.org/papers/HICOMB2004-06.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Quality Education","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1523895109","https://openalex.org/W1822105579","https://openalex.org/W1978470410","https://openalex.org/W2009570821","https://openalex.org/W2011368877","https://openalex.org/W2015292449","https://openalex.org/W2023206235","https://openalex.org/W2029475416","https://openalex.org/W2055043387","https://openalex.org/W2064345118","https://openalex.org/W2073865971","https://openalex.org/W2075871133","https://openalex.org/W2106882534","https://openalex.org/W2108215151","https://openalex.org/W2141885858","https://openalex.org/W2149429041","https://openalex.org/W2156492633","https://openalex.org/W2158381555","https://openalex.org/W2173952877","https://openalex.org/W2610552050","https://openalex.org/W4236236547","https://openalex.org/W4245668478","https://openalex.org/W4250052351","https://openalex.org/W6631470506"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2141411672","https://openalex.org/W2111937814","https://openalex.org/W2759306076","https://openalex.org/W1482324242","https://openalex.org/W187239587","https://openalex.org/W2730968108","https://openalex.org/W4386770652","https://openalex.org/W2158700816","https://openalex.org/W2055553856"],"abstract_inverted_index":{"Summary":[0],"form":[1],"only":[2],"given.":[3],"With":[4],"the":[5,67,97],"growing":[6],"number":[7],"of":[8,17,58,69,95],"known":[9],"RNA":[10,18,36,44,72],"genes":[11],"efficient":[12],"and":[13,104],"accurate":[14],"computational":[15],"analysis":[16],"sequences":[19],"is":[20],"becoming":[21],"increasingly":[22],"important.":[23],"Stochastic":[24],"context-free":[25],"grammars":[26],"(SCFGs)":[27],"are":[28,49],"used":[29],"as":[30,101],"a":[31,70,79],"popular":[32],"tool":[33],"to":[34,46,60,83,91],"model":[35],"secondary":[37],"structures.":[38],"However,":[39],"algorithms":[40],"for":[41],"aligning":[42],"an":[43,47],"sequence":[45],"SCFG":[48],"highly":[50],"compute-intensive.":[51],"This":[52,87],"has":[53],"so":[54],"far":[55],"limited":[56],"applications":[57],"SCFGs":[59],"relatively":[61],"small":[62],"problem":[63],"sizes.":[64],"We":[65],"present":[66],"design":[68],"parallel":[71],"sequence-structure":[73,93],"alignment":[74],"algorithm.":[75],"Its":[76],"implementation":[77],"on":[78],"PC":[80],"cluster":[81],"leads":[82],"significant":[84],"runtime":[85],"savings.":[86],"makes":[88],"it":[89],"possible":[90],"compute":[92],"alignments":[94],"even":[96],"largest":[98],"RNAs":[99],"such":[100],"SSU":[102],"rRNAs":[103,106],"LSU":[105],"in":[107],"reasonable":[108],"time.":[109]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
