{"id":"https://openalex.org/W2901938264","doi":"https://doi.org/10.1109/iccabs.2018.8541897","title":"Faster Computation of Genome Mappability with one Mismatch","display_name":"Faster Computation of Genome Mappability with one Mismatch","publication_year":2018,"publication_date":"2018-10-01","ids":{"openalex":"https://openalex.org/W2901938264","doi":"https://doi.org/10.1109/iccabs.2018.8541897","mag":"2901938264"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2018.8541897","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2018.8541897","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5048746537","display_name":"Sahar Hooshmand","orcid":null},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sahar Hooshmand","raw_affiliation_strings":["dept. of Computer Science, University of Central Florida, Orlando, FL, USA"],"affiliations":[{"raw_affiliation_string":"dept. of Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034779222","display_name":"Paniz Abedin","orcid":"https://orcid.org/0000-0001-7854-7960"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paniz Abedin","raw_affiliation_strings":["dept. of Computer Science, University of Central Florida, Orlando, FL, USA"],"affiliations":[{"raw_affiliation_string":"dept. of Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026282036","display_name":"Daniel Gibney","orcid":"https://orcid.org/0000-0003-1493-5432"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Gibney","raw_affiliation_strings":["dept. of Computer Science, University of Central Florida, Orlando, FL, USA"],"affiliations":[{"raw_affiliation_string":"dept. of Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074347913","display_name":"Srinivas Aluru","orcid":"https://orcid.org/0000-0003-4279-469X"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Srinivas Aluru","raw_affiliation_strings":["dept. of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA"],"affiliations":[{"raw_affiliation_string":"dept. of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049669178","display_name":"Sharma V. Thankachan","orcid":"https://orcid.org/0000-0002-6852-1035"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sharma V. Thankachan","raw_affiliation_strings":["dept. of Computer Science, University of Central Florida, Orlando, FL, USA"],"affiliations":[{"raw_affiliation_string":"dept. of Computer Science, University of Central Florida, Orlando, FL, USA","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5048746537"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":null,"apc_paid":null,"fwci":0.1629,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.60370042,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.996999979019165,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.996999979019165,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/substring","display_name":"Substring","score":0.6901160478591919},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.6276416778564453},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.6202031970024109},{"id":"https://openalex.org/keywords/hamming-distance","display_name":"Hamming distance","score":0.5844627022743225},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.5733039975166321},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.4867672920227051},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4626646041870117},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.44433116912841797},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38840076327323914},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3541891574859619},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.34924811124801636},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.34877878427505493},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.15382465720176697},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10740455985069275},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10020798444747925},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08070474863052368}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.6901160478591919},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.6276416778564453},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.6202031970024109},{"id":"https://openalex.org/C193319292","wikidata":"https://www.wikidata.org/wiki/Q272172","display_name":"Hamming distance","level":2,"score":0.5844627022743225},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.5733039975166321},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.4867672920227051},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4626646041870117},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.44433116912841797},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38840076327323914},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3541891574859619},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.34924811124801636},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.34877878427505493},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.15382465720176697},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10740455985069275},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10020798444747925},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08070474863052368},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2018.8541897","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2018.8541897","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":4,"referenced_works":["https://openalex.org/W2018742603","https://openalex.org/W2614077859","https://openalex.org/W2794525315","https://openalex.org/W6749857160"],"related_works":["https://openalex.org/W2070949798","https://openalex.org/W96331545","https://openalex.org/W2102450363","https://openalex.org/W2162655434","https://openalex.org/W3022344494","https://openalex.org/W1548907175","https://openalex.org/W1608420182","https://openalex.org/W2583658747","https://openalex.org/W1674453943","https://openalex.org/W3127593639"],"abstract_inverted_index":{"Summary":[0],"form":[1],"only":[2],"given.":[3],"The":[4,154,184],"genome":[5,130],"mappability":[6],"problem":[7,38,125],"refers":[8],"to":[9,28,34],"cataloging":[10],"repetitive":[11],"occurrences":[12],"of":[13,16,48,129,167],"every":[14],"substring":[15],"length":[17,49],"m":[18,67,96,102],"in":[19],"a":[20,44,137],"genome,":[21],"and":[22,62,66,151,169],"its":[23],"k-mappability":[24],"variant":[25],"extends":[26],"this":[27,124,133],"approximate":[29],"repeats":[30],"by":[31,178],"allowing":[32],"up":[33],"k":[35,65],"mismatches.":[36],"This":[37],"is":[39,157,173,190],"formulated":[40],"as":[41],"follows:":[42],"Given":[43],"sequence":[45],"S[1,":[46],"n]":[47],"n":[50,193],"over":[51],"the":[52,114,127,158,163,170,176],"constant":[53],"DNA":[54],"alphabet":[55],"\u03a3":[56],"=":[57,86],"{A,":[58],"C,":[59],"G,":[60],"T},":[61],"two":[63],"integers":[64],"\u2264":[68,105],"n,":[69],"output":[70],"an":[71],"integer":[72],"array":[73],"F":[74,81],"<sub":[75,82,90,109],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[76,83,91,110],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">k</sub>":[77,84],",":[78],"such":[79],"that:":[80],"[i]":[85],"|{j":[87],"\u2260":[88],"i|d":[89],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">H</sub>":[92,111],"(S[i,":[93],"i":[94],"+":[95,101],"-":[97,103],"1],":[98],"S[j,":[99],"j":[100],"1])":[104],"k}|":[106],"where":[107],"d":[108],"(\u00b7,\u00b7)":[112],"represents":[113],"hamming":[115],"distance.":[116],"Derrien":[117],"et":[118,180,198],"al.":[119,181],"[PLoS":[120],"one":[121],"2012]":[122],"represented":[123],"within":[126],"framework":[128,177],"analysis.":[131],"In":[132],"work":[134,172],"we":[135],"present":[136],"provably":[138],"efficient":[139],"algorithm":[140],"for":[141],"1-mappability":[142],"with":[143],"O(n":[144,191],"log":[145,192,194,195],"n)":[146,196],"worst":[147],"case":[148],"run":[149,188],"time":[150,189],"O(n)":[152],"spece.":[153],"fundamental":[155],"technique":[156],"heavy":[159],"path":[160],"decomposition":[161],"on":[162,175],"suffix":[164],"tree":[165],"(ST)":[166],"S,":[168],"entire":[171],"based":[174],"Thankachan":[179],"[RECOMB":[182],"2018].":[183],"previous":[185],"best":[186],"known":[187],"[Alzamel":[197],"al.,":[199],"COCOA":[200],"2017].":[201]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}