{"id":"https://openalex.org/W2154340429","doi":"https://doi.org/10.1093/bioinformatics/btl057","title":"Recco: recombination analysis using cost optimization","display_name":"Recco: recombination analysis using cost optimization","publication_year":2006,"publication_date":"2006-02-17","ids":{"openalex":"https://openalex.org/W2154340429","doi":"https://doi.org/10.1093/bioinformatics/btl057","mag":"2154340429","pmid":"https://pubmed.ncbi.nlm.nih.gov/16488909"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl057","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl057","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055659347","display_name":"Jochen Maydt","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109712","display_name":"Max Planck Institute for Informatics","ror":"https://ror.org/01w19ak89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jochen Maydt","raw_affiliation_strings":["Max-Planck Institut f\u00fcr Informatik \u00a0 Saarbr\u00fccken, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max-Planck Institut f\u00fcr Informatik \u00a0 Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210109712"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023556977","display_name":"Thomas Lengauer","orcid":"https://orcid.org/0000-0003-3801-2640"},"institutions":[{"id":"https://openalex.org/I4210109712","display_name":"Max Planck Institute for Informatics","ror":"https://ror.org/01w19ak89","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210109712"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Lengauer","raw_affiliation_strings":["Max-Planck Institut f\u00fcr Informatik \u00a0 Saarbr\u00fccken, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max-Planck Institut f\u00fcr Informatik \u00a0 Saarbr\u00fccken, Germany","institution_ids":["https://openalex.org/I4210109712"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5055659347"],"corresponding_institution_ids":["https://openalex.org/I4210109712"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.8484,"has_fulltext":false,"cited_by_count":118,"citation_normalized_percentile":{"value":0.8443041,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"9","first_page":"1064","last_page":"1071"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9932000041007996,"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/recombination","display_name":"Recombination","score":0.8370141983032227},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5916956067085266},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5736443400382996},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.5170536637306213},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5093594789505005},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36829718947410583},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35079944133758545},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3411545157432556},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33115440607070923},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2081374228000641}],"concepts":[{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.8370141983032227},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5916956067085266},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5736443400382996},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.5170536637306213},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5093594789505005},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36829718947410583},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35079944133758545},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3411545157432556},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33115440607070923},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2081374228000641},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btl057","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl057","pdf_url":null,"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:16488909","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16488909","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:CiteSeerX.psu:10.1.1.103.2563","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.103.2563","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/btl057v1.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.333.8135","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.333.8135","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/content/22/9/1064.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.98.6758","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.98.6758","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/22/9/1064.pdf","raw_type":"text"},{"id":"pmh:oai:edoc.mpg.de:314608","is_oa":false,"landing_page_url":"http://edoc.mpg.de/314608","pdf_url":null,"source":{"id":"https://openalex.org/S4406922265","display_name":"Max Planck Institute for Plasma Physics","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":"Bioinformatics, v.22, 1064-1071 (2006)","raw_type":"Article"},{"id":"pmh:oai:pure.mpg.de:item_1328527","is_oa":false,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-000F-23CD-A","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8399999737739563,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W114397555","https://openalex.org/W160666045","https://openalex.org/W590116524","https://openalex.org/W1525734744","https://openalex.org/W1566688548","https://openalex.org/W1579352620","https://openalex.org/W1880845650","https://openalex.org/W1920471162","https://openalex.org/W1973667633","https://openalex.org/W1987646246","https://openalex.org/W2007735554","https://openalex.org/W2007849128","https://openalex.org/W2026152438","https://openalex.org/W2029011467","https://openalex.org/W2042789248","https://openalex.org/W2048285065","https://openalex.org/W2064251379","https://openalex.org/W2065461553","https://openalex.org/W2069081220","https://openalex.org/W2072362336","https://openalex.org/W2075371279","https://openalex.org/W2091181646","https://openalex.org/W2097276024","https://openalex.org/W2100243754","https://openalex.org/W2105017262","https://openalex.org/W2106101113","https://openalex.org/W2110065044","https://openalex.org/W2124375095","https://openalex.org/W2124877203","https://openalex.org/W2125359798","https://openalex.org/W2134595458","https://openalex.org/W2136817755","https://openalex.org/W2147660889","https://openalex.org/W2148889460","https://openalex.org/W2159866605","https://openalex.org/W2163400707","https://openalex.org/W2165601275","https://openalex.org/W2171022989","https://openalex.org/W2172142645","https://openalex.org/W2978522494","https://openalex.org/W6606503875","https://openalex.org/W6678804063","https://openalex.org/W6684738558"],"related_works":["https://openalex.org/W2180954594","https://openalex.org/W2052835778","https://openalex.org/W2049003611","https://openalex.org/W2127804977","https://openalex.org/W2108418243","https://openalex.org/W164103134","https://openalex.org/W2787352659","https://openalex.org/W1970611213","https://openalex.org/W1707372784","https://openalex.org/W2096006843"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recombination":[1],"plays":[2],"an":[3,73],"important":[4],"role":[5],"in":[6,124],"the":[7,54,60,63,83,92,104,131],"evolution":[8],"of":[9,32,56,59,91,103,127],"many":[10],"pathogens,":[11],"such":[12],"as":[13,111],"HIV":[14],"or":[15],"malaria.":[16],"Despite":[17],"substantial":[18],"prior":[19],"work,":[20],"there":[21],"is":[22,122],"still":[23],"a":[24,43,49],"pressing":[25],"need":[26],"for":[27,77],"efficient":[28],"and":[29,35,67],"effective":[30],"methods":[31],"detecting":[33,128],"recombination":[34,79,96,129,139],"analyzing":[36],"recombinant":[37],"sequences.":[38],"RESULTS:":[39],"We":[40,81],"introduce":[41],"Recco,":[42],"novel":[44],"fast":[45],"method":[46],"that,":[47],"given":[48],"multiple":[50],"sequence":[51,84,114],"alignment,":[52],"scores":[53],"cost":[55,97,106],"obtaining":[57],"one":[58],"sequences":[61],"from":[62],"others":[64],"by":[65],"mutation":[66,99],"recombination.":[68],"The":[69,101],"algorithm":[70,132],"comes":[71],"with":[72,86,130],"illustrative":[74],"visualization":[75],"tool":[76],"locating":[78],"breakpoints.":[80],"analyze":[82],"alignment":[85],"respect":[87],"to":[88,112],"all":[89],"choices":[90],"parameter":[93],"alpha":[94],"weighting":[95],"against":[98],"cost.":[100],"analysis":[102],"resulting":[105],"curve":[107],"yields":[108],"additional":[109],"information":[110],"which":[113],"might":[115],"be":[116],"recombinant.":[117],"On":[118],"random":[119],"genealogies":[120],"Recco":[121,141],"comparable":[123],"its":[125],"power":[126],"Geneconv":[133],"(Sawyer,":[134],"1989).":[135],"For":[136],"specific":[137],"relevant":[138],"scenarios":[140],"significantly":[142],"outperforms":[143],"Geneconv.":[144]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":9}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
