{"id":"https://openalex.org/W4239428642","doi":"https://doi.org/10.1093/bioinformatics/btr647","title":"Sensitive and fast mapping of di-base encoded reads","display_name":"Sensitive and fast mapping of di-base encoded reads","publication_year":2011,"publication_date":"2011-12-21","ids":{"openalex":"https://openalex.org/W4239428642","doi":"https://doi.org/10.1093/bioinformatics/btr647"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr647","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr647","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/1/150/593659/btr647.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/28/1/150/593659/btr647.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016230870","display_name":"Farhad Hormozdiari","orcid":"https://orcid.org/0000-0002-5617-6174"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Farhad Hormozdiari","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I18014758","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006644128","display_name":"Faraz Hach","orcid":"https://orcid.org/0000-0003-1143-0172"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Faraz Hach","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I18014758","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102972238","display_name":"S. Cenk \u015eahinalp","orcid":"https://orcid.org/0000-0002-2170-2808"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"S. Cenk Sahinalp","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I18014758","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014870107","display_name":"Evan E. Eichler","orcid":"https://orcid.org/0000-0002-8246-4014"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Evan E. Eichler","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I18014758","https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074885623","display_name":"Can Alkan","orcid":"https://orcid.org/0000-0002-5443-0706"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Can Alkan","raw_affiliation_strings":["1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Genome Sciences, University of Washington, and Howard Hughes Medical Institute, Seattle, WA, USA and 2Simon Fraser University, School of Computing Science, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I18014758","https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.3277877,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":93},"biblio":{"volume":"28","issue":"1","first_page":"150","last_page":"150"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9556999802589417,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9556999802589417,"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/computer-science","display_name":"Computer science","score":0.6339048147201538},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.624997615814209},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44175440073013306},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.420342355966568},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24421721696853638},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1926400363445282},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1335912048816681}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6339048147201538},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.624997615814209},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44175440073013306},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.420342355966568},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24421721696853638},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1926400363445282},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1335912048816681},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btr647","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr647","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/1/150/593659/btr647.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:pubmedcentral.nih.gov:3276229","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3276229","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr647","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr647","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/1/150/593659/btr647.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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2356158875","https://openalex.org/W2367699234","https://openalex.org/W2347547156","https://openalex.org/W2360518820","https://openalex.org/W2367717118","https://openalex.org/W3199334028","https://openalex.org/W2410461802","https://openalex.org/W2384034920","https://openalex.org/W2352137971","https://openalex.org/W2380722574"],"abstract_inverted_index":{"Bioinformatics":[0],"(2011)":[1],"27(4),":[2],"1915\u20131921.":[3],"The":[4],"authors":[5],"find":[6],"it":[7],"worth":[8],"mentioning":[9],"that":[10],"the":[11,16,28,32,38,132,150,167,199],"parameters":[12,48,169,201],"used":[13,37,85,137],"to":[14,22,111,129,141],"run":[15],"PerM":[17,42,95,109,162,194],"mapper":[18],"were":[19],"not":[20],"optimal":[21],"achieve":[23],"full":[24,98],"sensitivity.":[25],"Based":[26],"on":[27],"new":[29,168,200],"recommendations":[30],"of":[31,34,41,61,69,144,161,193],"developers":[33],"PerM,":[35,139],"we":[36,83,136],"latest":[39],"version":[40],"(v.":[43],"0.3.6),":[44],"and":[45,124,156],"updated":[46],"two":[47],"as":[49,158],"follows:":[50],"\u2013seed":[51],"F2":[52],"(full":[53],"sensitivity":[54,99],"for":[55,71,79,131,138],"1":[56,64],"SNPs);":[57],"-v":[58,90],"2":[59],"(number":[60],"mismatches);":[62],"-k":[63,88],"000":[65,66],"(maximum":[67],"number":[68],"alignment":[70],"a":[72,80],"read);":[73],"-A":[74],"(report":[75],"all":[76],"possible":[77],"mapping":[78],"reads).":[81],"Previously,":[82],"have":[84],"\u2018\u2013seed":[86],"S20":[87],"10000":[89],"4\u2019.":[91],"With":[92,104],"this":[93],"update,":[94],"now":[96,148],"achieves":[97],"in":[100,153],"our":[101,142],"simulation":[102],"experiment.":[103],"real":[105,196],"datasets":[106,165,197],"(Table":[107],"6),":[108],"tends":[110],"map":[112],"more":[113],"reads":[114],"compared":[115],"with":[116,163,195],"Bowtie,":[117],"but":[118],"maps":[119],"slightly":[120],"less":[121],"than":[122],"Mapreads":[123],"SOCS.":[125],"We":[126,147],"would":[127],"like":[128],"apologize":[130],"previous":[133],"parameter":[134],"sets":[135],"due":[140],"misinterpretation":[143],"its":[145],"documentation.":[146],"update":[149],"relevant":[151],"rows":[152],"Tables":[154],"3":[155],"6":[157],"follows.":[159],"Performance":[160,192],"simulated":[164,172],"considering":[166],"Reads":[170],"are":[171],"from":[173],"human":[174],"reference":[175],"genome":[176],"build":[177],"35":[178],"(chromosome":[179],"1).":[180],"Set":[181,185,189],"1:":[182],"no":[183],"errors;":[184,188],"2:":[186],"color":[187],"3:":[190],"substitutions.":[191],"using":[198]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
