{"id":"https://openalex.org/W2115872073","doi":"https://doi.org/10.1093/bioinformatics/btp486","title":"PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds","display_name":"PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds","publication_year":2009,"publication_date":"2009-08-12","ids":{"openalex":"https://openalex.org/W2115872073","doi":"https://doi.org/10.1093/bioinformatics/btp486","mag":"2115872073"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp486","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/19/2514/48995397/bioinformatics_25_19_2514.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"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/19/2514/48995397/bioinformatics_25_19_2514.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045064581","display_name":"Yangho Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yangho Chen","raw_affiliation_strings":["Program in Computational Biology and Bioinformatics, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA"],"affiliations":[{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029982769","display_name":"Tade Souaiaia","orcid":"https://orcid.org/0000-0003-3922-1372"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tade Souaiaia","raw_affiliation_strings":["Program in Computational Biology and Bioinformatics, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA"],"affiliations":[{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100443173","display_name":"Ting Chen","orcid":"https://orcid.org/0000-0001-8414-6346"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ting Chen","raw_affiliation_strings":["Program in Computational Biology and Bioinformatics, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA"],"affiliations":[{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5045064581"],"corresponding_institution_ids":["https://openalex.org/I1174212"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.6609,"has_fulltext":true,"cited_by_count":120,"citation_normalized_percentile":{"value":0.96836248,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"25","issue":"19","first_page":"2514","last_page":"2521"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9977999925613403,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/byte","display_name":"Byte","score":0.7387447357177734},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6735255718231201},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6594642400741577},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.5911623239517212},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.584827721118927},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4903907775878906},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4281070828437805},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4157119393348694},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.41198480129241943},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22019487619400024},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.13090172410011292},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12955039739608765},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12609976530075073}],"concepts":[{"id":"https://openalex.org/C43364308","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Byte","level":2,"score":0.7387447357177734},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6735255718231201},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6594642400741577},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.5911623239517212},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.584827721118927},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4903907775878906},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4281070828437805},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4157119393348694},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.41198480129241943},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22019487619400024},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.13090172410011292},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12955039739608765},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12609976530075073},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp486","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/19/2514/48995397/bioinformatics_25_19_2514.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":"pmh:oai:CiteSeerX.psu:10.1.1.215.7618","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.215.7618","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/btp486v1.pdf","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2752623","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2752623","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp486","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/19/2514/48995397/bioinformatics_25_19_2514.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":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2115872073.pdf","grobid_xml":"https://content.openalex.org/works/W2115872073.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1606551583","https://openalex.org/W1658221551","https://openalex.org/W1873119440","https://openalex.org/W1955121107","https://openalex.org/W1986473212","https://openalex.org/W1987857466","https://openalex.org/W2012385440","https://openalex.org/W2053773712","https://openalex.org/W2055043387","https://openalex.org/W2061680337","https://openalex.org/W2065579185","https://openalex.org/W2072193858","https://openalex.org/W2096760403","https://openalex.org/W2097862362","https://openalex.org/W2100751585","https://openalex.org/W2101286050","https://openalex.org/W2101664494","https://openalex.org/W2103441770","https://openalex.org/W2103706581","https://openalex.org/W2111858824","https://openalex.org/W2112113834","https://openalex.org/W2121211805","https://openalex.org/W2124985265","https://openalex.org/W2128591967","https://openalex.org/W2131989567","https://openalex.org/W2136145671","https://openalex.org/W2139371638","https://openalex.org/W2139760555","https://openalex.org/W2143124024","https://openalex.org/W2153527981","https://openalex.org/W2162277333","https://openalex.org/W2167677447","https://openalex.org/W4243977291","https://openalex.org/W4293196852","https://openalex.org/W6643069710","https://openalex.org/W6653382061","https://openalex.org/W6684867979","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W3042604642","https://openalex.org/W121858127","https://openalex.org/W2165263102","https://openalex.org/W4289329995","https://openalex.org/W2373574911","https://openalex.org/W2775143306","https://openalex.org/W2046727832","https://openalex.org/W2012747176","https://openalex.org/W4247895841","https://openalex.org/W2107233609"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"The":[2,91],"explosion":[3],"of":[4,12,48,54],"next-generation":[5],"sequencing":[6,27],"data":[7,57,92,178],"has":[8],"spawned":[9],"the":[10,64,104,122,146,155],"design":[11],"new":[13],"algorithms":[14],"and":[15,26,50,136,141,168],"software":[16],"tools":[17],"to":[18,43,77,102,110,113,121,133],"provide":[19],"efficient":[20],"mapping":[21,65,80,164],"for":[22,82,131,139,166],"different":[23],"read":[24],"lengths":[25],"technologies.":[28],"In":[29],"particular,":[30],"ABI's":[31],"sequencer":[32],"(SOLiD":[33],"system)":[34],"poses":[35],"a":[36,162],"big":[37],"computational":[38],"challenge":[39],"with":[40,88],"its":[41,51],"capacity":[42],"produce":[44],"very":[45],"large":[46,83],"amounts":[47],"data,":[49],"unique":[52],"strategy":[53],"encoding":[55],"sequence":[56],"into":[58],"color":[59],"signals.":[60],"Results:":[61],"We":[62],"present":[63],"software,":[66],"named":[67],"PerM":[68,95,161],"(Periodic":[69],"Seed":[70],"Mapping)":[71],"that":[72],"uses":[73],"periodic":[74,126],"spaced":[75],"seeds":[76,127],"significantly":[78,152],"improve":[79],"efficiency":[81],"reference":[84],"genomes":[85,109],"when":[86],"compared":[87],"state-of-the-art":[89],"programs.":[90],"structure":[93],"in":[94],"requires":[96],"only":[97],"4.5":[98],"bytes":[99],"per":[100,150],"base":[101],"index":[103],"human":[105],"genome,":[106],"allowing":[107],"entire":[108],"be":[111],"loaded":[112],"memory,":[114],"while":[115,144],"multiple":[116],"processors":[117],"simultaneously":[118],"map":[119],"reads":[120],"reference.":[123],"Weight":[124],"maximized":[125],"offer":[128],"full":[129],"sensitivity":[130,138,159],"up":[132,154],"three":[134],"mismatches":[135,143],"high":[137],"four":[140],"five":[142],"minimizing":[145],"number":[147],"random":[148],"hits":[149],"query,":[151],"speeding":[153],"running":[156],"time.":[157],"Such":[158],"makes":[160],"valuable":[163],"tool":[165],"SOLiD":[167],"Solexa":[169],"reads.":[170],"Availability:":[171],"http://code.google.com/p/perm/":[172],"Contact:":[173],"tingchen@usc.edu":[174],"Supplementary":[175,177],"information:":[176],"are":[179],"available":[180],"at":[181],"Bioinformatics":[182],"online.":[183]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":19},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":11}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
