{"id":"https://openalex.org/W2162786061","doi":"https://doi.org/10.1093/bioinformatics/btr537","title":"Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection","display_name":"Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection","publication_year":2011,"publication_date":"2011-10-05","ids":{"openalex":"https://openalex.org/W2162786061","doi":"https://doi.org/10.1093/bioinformatics/btr537","mag":"2162786061","pmid":"https://pubmed.ncbi.nlm.nih.gov/21976422"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr537","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr537","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/22/3085/48861498/bioinformatics_27_22_3085.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/27/22/3085/48861498/bioinformatics_27_22_3085.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025857432","display_name":"Michiaki Hamada","orcid":"https://orcid.org/0000-0001-9466-1034"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Michiaki Hamada","raw_affiliation_strings":["1 Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562 and 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562 and 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009819704","display_name":"Edward Wijaya","orcid":"https://orcid.org/0000-0002-1234-0761"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Edward Wijaya","raw_affiliation_strings":["1 Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562 and 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562 and 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055829507","display_name":"Martin C. Frith","orcid":"https://orcid.org/0000-0003-0998-2859"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Martin C. Frith","raw_affiliation_strings":["1 Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562 and 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562 and 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082068847","display_name":"Kiyoshi Asai","orcid":"https://orcid.org/0000-0003-0909-4982"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kiyoshi Asai","raw_affiliation_strings":["1 Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562 and 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Graduate School of Frontier Sciences, University of Tokyo, 5\u20131\u20135 Kashiwanoha, Kashiwa 277\u20138562 and 2Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2\u201341\u20136, Aomi, Koto-ku, Tokyo 135\u20130064, Japan","institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5025857432"],"corresponding_institution_ids":["https://openalex.org/I73613424","https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.0372,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.87336932,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"27","issue":"22","first_page":"3085","last_page":"3092"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.41780000925064087,"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"}},"topics":[{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.41780000925064087,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.30140000581741333,"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":0.16040000319480896,"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/indel","display_name":"Indel","score":0.8816537857055664},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.65088951587677},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.6265158653259277},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.6169288158416748},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.43026331067085266},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3770795464515686},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3452634811401367},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2669324278831482},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21158510446548462},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.1235710084438324},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09132155776023865}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.8816537857055664},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.65088951587677},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.6265158653259277},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.6169288158416748},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.43026331067085266},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3770795464515686},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3452634811401367},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2669324278831482},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21158510446548462},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.1235710084438324},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09132155776023865},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","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":"D017422","descriptor_name":"Sequence Analysis, DNA","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":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btr537","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr537","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/22/3085/48861498/bioinformatics_27_22_3085.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:21976422","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21976422","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":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/22/3085","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/22/3085","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr537","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr537","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/22/3085/48861498/bioinformatics_27_22_3085.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":[{"id":"https://openalex.org/G8124787675","display_name":"Platform of large scale and high quality genomics and bioinformatics: Towards the advancement of genome sciences in academia","funder_award_id":"221S0002","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1513515886","https://openalex.org/W1866859902","https://openalex.org/W1971376828","https://openalex.org/W1997631042","https://openalex.org/W2007135806","https://openalex.org/W2037113830","https://openalex.org/W2044250973","https://openalex.org/W2052158622","https://openalex.org/W2058839892","https://openalex.org/W2067151470","https://openalex.org/W2069689025","https://openalex.org/W2072193858","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2087464200","https://openalex.org/W2097862362","https://openalex.org/W2103441770","https://openalex.org/W2105035271","https://openalex.org/W2107164256","https://openalex.org/W2108234281","https://openalex.org/W2111584304","https://openalex.org/W2112113834","https://openalex.org/W2115872073","https://openalex.org/W2118581189","https://openalex.org/W2120748415","https://openalex.org/W2124985265","https://openalex.org/W2128524432","https://openalex.org/W2128793361","https://openalex.org/W2131016694","https://openalex.org/W2133212095","https://openalex.org/W2133956160","https://openalex.org/W2140154634","https://openalex.org/W2143173327","https://openalex.org/W2143697424","https://openalex.org/W2158714788","https://openalex.org/W2161224111","https://openalex.org/W2161815151","https://openalex.org/W2162758337","https://openalex.org/W2170945060","https://openalex.org/W2171777347","https://openalex.org/W2781191471","https://openalex.org/W2885727518","https://openalex.org/W3214380909","https://openalex.org/W4245668478","https://openalex.org/W6665478942"],"related_works":["https://openalex.org/W2033001683","https://openalex.org/W2167094946","https://openalex.org/W4387460329","https://openalex.org/W2046457574","https://openalex.org/W1949458596","https://openalex.org/W4285059642","https://openalex.org/W3144677376","https://openalex.org/W32785519","https://openalex.org/W4382398022","https://openalex.org/W2164863064"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"studies":[2],"have":[3],"revealed":[4],"the":[5,62,105],"importance":[6],"of":[7,11,78,95,102,133,148,166],"considering":[8],"quality":[9,58,100,136],"scores":[10,59,101],"reads":[12],"generated":[13],"by":[14],"next-generation":[15],"sequence":[16],"(NGS)":[17],"platforms":[18],"in":[19,69,85,122],"various":[20,124],"downstream":[21],"analyses.":[22,87],"It":[23],"is":[24,64,83,116,156],"also":[25,197],"known":[26],"that":[27,56,98,174,199],"probabilistic":[28,54,96,131,175],"alignments":[29,134,176],"based":[30,117],"on":[31,118],"marginal":[32,125],"probabilities":[33,126],"(e.g.":[34],"aligned-column":[35],"and/or":[36],"gap":[37],"probabilities)":[38],"provide":[39],"more":[40],"accurate":[41,76,164],"alignment":[42,55,97],"than":[43],"conventional":[44],"maximum":[45],"score-based":[46],"alignment.":[47],"There":[48],"exists,":[49],"however,":[50],"no":[51],"study":[52,196],"about":[53],"considers":[57],"explicitly,":[60],"although":[61],"method":[63,115,155],"expected":[65],"to":[66,159],"be":[67],"useful":[68],"SNP/indel":[70,206],"callers":[71],"and":[72,138,143,152,168,181,193],"bisulfite":[73],"mapping,":[74],"because":[75],"estimation":[77],"aligned":[79,179],"columns":[80,151,180],"or":[81],"gaps":[82,182],"important":[84],"those":[86],"RESULTS:":[88],"In":[89],"this":[90],"study,":[91],"we":[92],"propose":[93],"methods":[94],"consider":[99],"(one":[103],"of)":[104],"sequences":[106],"as":[107,109],"well":[108],"a":[110,130],"usual":[111],"score":[112],"matrix.":[113],"The":[114,154,195],"posterior":[119],"decoding":[120],"techniques":[121],"which":[123],"are":[127],"computed":[128],"from":[129],"model":[132],"with":[135,185],"scores,":[137],"can":[139,177],"arbitrarily":[140],"trade-off":[141],"sensitivity":[142],"positive":[144],"predictive":[145],"value":[146],"(PPV)":[147],"prediction":[149],"(aligned":[150],"gaps).":[153],"directly":[157],"applicable":[158],"read":[160],"mapping":[161,187],"(alignment)":[162],"toward":[163],"detection":[165],"SNPs":[167],"indels.":[169],"Several":[170],"computational":[171],"experiments":[172],"indicated":[173],"estimate":[178],"accurately,":[183],"compared":[184],"other":[186],"algorithms":[188],"e.g.":[189],"SHRiMP2,":[190],"Stampy,":[191],"BWA":[192],"Novoalign.":[194],"suggested":[198],"our":[200],"approach":[201],"yields":[202],"favorable":[203],"precision":[204],"for":[205],"calling.":[207]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
