{"id":"https://openalex.org/W2139760555","doi":"https://doi.org/10.1093/bioinformatics/btn025","title":"SOAP: short oligonucleotide alignment program","display_name":"SOAP: short oligonucleotide alignment program","publication_year":2008,"publication_date":"2008-01-28","ids":{"openalex":"https://openalex.org/W2139760555","doi":"https://doi.org/10.1093/bioinformatics/btn025","mag":"2139760555","pmid":"https://pubmed.ncbi.nlm.nih.gov/18227114"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn025","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn025","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/713/49052204/bioinformatics_24_5_713.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/24/5/713/49052204/bioinformatics_24_5_713.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038736219","display_name":"Ruiqiang Li","orcid":"https://orcid.org/0000-0003-4760-1535"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["CN","DK"],"is_corresponding":false,"raw_author_name":"Ruiqiang Li","raw_affiliation_strings":["1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark","institution_ids":["https://openalex.org/I100135526","https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064592001","display_name":"Yingrui Li","orcid":"https://orcid.org/0000-0001-6630-1277"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["CN","DK"],"is_corresponding":false,"raw_author_name":"Yingrui Li","raw_affiliation_strings":["1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark","institution_ids":["https://openalex.org/I100135526","https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017132939","display_name":"Karsten Kristiansen","orcid":"https://orcid.org/0000-0002-6024-0917"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["CN","DK"],"is_corresponding":false,"raw_author_name":"Karsten Kristiansen","raw_affiliation_strings":["1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark","institution_ids":["https://openalex.org/I100135526","https://openalex.org/I177969490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111964102","display_name":"Jun Wang","orcid":"https://orcid.org/0009-0008-8475-2934"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["CN","DK"],"is_corresponding":true,"raw_author_name":"Jun Wang","raw_affiliation_strings":["1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China and 2Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, DK-5230, Denmark","institution_ids":["https://openalex.org/I100135526","https://openalex.org/I177969490"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5111964102"],"corresponding_institution_ids":["https://openalex.org/I100135526","https://openalex.org/I177969490"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":52.3008,"has_fulltext":false,"cited_by_count":3781,"citation_normalized_percentile":{"value":0.99946473,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"5","first_page":"713","last_page":"714"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5992000102996826,"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":0.5992000102996826,"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":0.22869999706745148,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.015200000256299973,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/soap","display_name":"SOAP","score":0.7980908751487732},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7335403561592102},{"id":"https://openalex.org/keywords/oligonucleotide","display_name":"Oligonucleotide","score":0.6114474534988403},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.46761927008628845},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4289875626564026},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38609346747398376},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.16009363532066345},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15373295545578003},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12744185328483582},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.11882764101028442}],"concepts":[{"id":"https://openalex.org/C17881449","wikidata":"https://www.wikidata.org/wiki/Q189620","display_name":"SOAP","level":2,"score":0.7980908751487732},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7335403561592102},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.6114474534988403},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.46761927008628845},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4289875626564026},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38609346747398376},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.16009363532066345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15373295545578003},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12744185328483582},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.11882764101028442}],"mesh":[{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn025","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn025","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/713/49052204/bioinformatics_24_5_713.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:18227114","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18227114","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":"Journal Article"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:368473","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:sdu.dk:openaire_cris_publications/fdcd9be0-def0-11dc-860c-000ea68e967b","is_oa":false,"landing_page_url":"https://portal.findresearcher.sdu.dk/da/publications/fdcd9be0-def0-11dc-860c-000ea68e967b","pdf_url":null,"source":{"id":"https://openalex.org/S4306400423","display_name":"University of Southern Denmark Research Portal (University of Southern Denmark)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177969490","host_organization_name":"University of Southern Denmark","host_organization_lineage":["https://openalex.org/I177969490"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Li, R, Li, Y, Kristiansen, K & Wang, J 2008, 'SOAP : short oligonucleotide alignment program', Bioinformatics, vol. 24, no. 5, pp. 713-714. https://doi.org/10.1093/bioinformatics/btn025","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn025","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn025","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/5/713/49052204/bioinformatics_24_5_713.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":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2139760555.pdf"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2054880642","https://openalex.org/W2107233609","https://openalex.org/W2136145671","https://openalex.org/W2142619120","https://openalex.org/W2158714788","https://openalex.org/W4293196852","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W2378589653","https://openalex.org/W2064455827","https://openalex.org/W2168864397","https://openalex.org/W2390172341","https://openalex.org/W2001381219","https://openalex.org/W2387363590","https://openalex.org/W2052041934","https://openalex.org/W2057413717","https://openalex.org/W1983114052","https://openalex.org/W2140008189"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"have":[2],"developed":[3],"a":[4,63,73],"program":[5,20],"SOAP":[6,42,61],"for":[7,76],"efficient":[8],"gapped":[9],"and":[10,56,71],"ungapped":[11],"alignment":[12],"of":[13,28],"short":[14,29],"oligonucleotides":[15],"onto":[16],"reference":[17],"sequences.":[18],"The":[19],"is":[21,43,62],"designed":[22],"to":[23],"handle":[24],"the":[25,36],"huge":[26],"amounts":[27],"reads":[30],"generated":[31],"by":[32],"parallel":[33,69],"sequencing":[34,40],"using":[35],"new":[37],"generation":[38],"Illumina-Solexa":[39],"technology.":[41],"compatible":[44],"with":[45],"numerous":[46],"applications,":[47],"including":[48],"single-read":[49],"or":[50],"pair-end":[51],"resequencing,":[52],"small":[53],"RNA":[54],"discovery":[55],"mRNA":[57],"tag":[58],"sequence":[59],"mapping.":[60],"command-driven":[64],"program,":[65],"which":[66],"supports":[67],"multi-threaded":[68],"computing,":[70],"has":[72],"batch":[74],"module":[75],"multiple":[77],"query":[78],"sets.":[79],"AVAILABILITY:":[80],"http://soap.genomics.org.cn.":[81]},"counts_by_year":[{"year":2026,"cited_by_count":212},{"year":2025,"cited_by_count":296},{"year":2024,"cited_by_count":368},{"year":2023,"cited_by_count":272},{"year":2022,"cited_by_count":298},{"year":2021,"cited_by_count":316},{"year":2020,"cited_by_count":234},{"year":2019,"cited_by_count":175},{"year":2018,"cited_by_count":143},{"year":2017,"cited_by_count":151},{"year":2016,"cited_by_count":148},{"year":2015,"cited_by_count":199},{"year":2014,"cited_by_count":198},{"year":2013,"cited_by_count":197},{"year":2012,"cited_by_count":180}],"updated_date":"2026-09-01T08:31:24.195828","created_date":"2025-10-10T00:00:00"}