{"id":"https://openalex.org/W2062411870","doi":"https://doi.org/10.1186/1471-2105-13-s17-s10","title":"A hybrid method for the exact planted (l, d) motif finding problem and its parallelization","display_name":"A hybrid method for the exact planted (l, d) motif finding problem and its parallelization","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2062411870","doi":"https://doi.org/10.1186/1471-2105-13-s17-s10","mag":"2062411870","pmid":"https://pubmed.ncbi.nlm.nih.gov/23281969"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s17-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s17-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S17-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S17-S10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052114281","display_name":"Mostafa Abbas","orcid":"https://orcid.org/0000-0001-6781-5384"},"institutions":[{"id":"https://openalex.org/I1355163","display_name":"Sinai University","ror":"https://ror.org/01dd13a92","country_code":"EG","type":"education","lineage":["https://openalex.org/I1355163"]}],"countries":["EG"],"is_corresponding":true,"raw_author_name":"Mostafa M Abbas","raw_affiliation_strings":["Department of Basic Sciences, Faculty of Engineering, Sinai University, El-Arish, Egypt. mabbas@su.edu.eg","Department of Basic Sciences, Faculty of Engineering, Sinai University, El-Arish, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Basic Sciences, Faculty of Engineering, Sinai University, El-Arish, Egypt. mabbas@su.edu.eg","institution_ids":["https://openalex.org/I1355163"]},{"raw_affiliation_string":"Department of Basic Sciences, Faculty of Engineering, Sinai University, El-Arish, Egypt","institution_ids":["https://openalex.org/I1355163"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034508551","display_name":"Mohamed Abouelhoda","orcid":"https://orcid.org/0000-0002-3483-2644"},"institutions":[{"id":"https://openalex.org/I145487455","display_name":"Cairo University","ror":"https://ror.org/03q21mh05","country_code":"EG","type":"education","lineage":["https://openalex.org/I145487455"]},{"id":"https://openalex.org/I57629906","display_name":"Nile University","ror":"https://ror.org/03cg7cp61","country_code":"EG","type":"education","lineage":["https://openalex.org/I57629906"]}],"countries":["EG"],"is_corresponding":true,"raw_author_name":"Mohamed Abouelhoda","raw_affiliation_strings":["Center for Informatics Sciences, Nile University, Giza, Egypt","Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Informatics Sciences, Nile University, Giza, Egypt","institution_ids":["https://openalex.org/I57629906"]},{"raw_affiliation_string":"Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt","institution_ids":["https://openalex.org/I145487455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024925431","display_name":"Hazem M. Bahig","orcid":"https://orcid.org/0000-0001-9448-6168"},"institutions":[{"id":"https://openalex.org/I107720978","display_name":"Ain Shams University","ror":"https://ror.org/00cb9w016","country_code":"EG","type":"education","lineage":["https://openalex.org/I107720978"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Hazem M Bahig","raw_affiliation_strings":["Computer Science Division, Department of Mathematics, Faculty of Science, Ain ShamsUniversity, Cairo, 11566, Egypt","Computer Science Division, Department of Mathematics, Faculty of Science, Ain ShamsUniversity, Cairo, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Division, Department of Mathematics, Faculty of Science, Ain ShamsUniversity, Cairo, 11566, Egypt","institution_ids":["https://openalex.org/I107720978"]},{"raw_affiliation_string":"Computer Science Division, Department of Mathematics, Faculty of Science, Ain ShamsUniversity, Cairo, Egypt","institution_ids":["https://openalex.org/I107720978"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5034508551","https://openalex.org/A5052114281"],"corresponding_institution_ids":["https://openalex.org/I1355163","https://openalex.org/I145487455","https://openalex.org/I57629906"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.1046,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.75796024,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"13","issue":"S17","first_page":"S10","last_page":"S10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5530999898910522,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5530999898910522,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.16019999980926514,"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/T11269","display_name":"Algorithms and Data Compression","score":0.0632999986410141,"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/motif","display_name":"Motif (music)","score":0.7561506628990173},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5905343294143677},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5683935880661011},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4171425700187683},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39735913276672363},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29427263140678406},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21061262488365173},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1340816617012024},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10526081919670105},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.0770559012889862}],"concepts":[{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.7561506628990173},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5905343294143677},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5683935880661011},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4171425700187683},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39735913276672363},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29427263140678406},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21061262488365173},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1340816617012024},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10526081919670105},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0770559012889862},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-13-s17-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s17-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S17-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23281969","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23281969","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2521572","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3521218","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s17-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s17-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S17-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2062411870.pdf","grobid_xml":"https://content.openalex.org/works/W2062411870.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W120639177","https://openalex.org/W601739477","https://openalex.org/W626058384","https://openalex.org/W1486659038","https://openalex.org/W1518105754","https://openalex.org/W1571755427","https://openalex.org/W1580213736","https://openalex.org/W1583782919","https://openalex.org/W1594947347","https://openalex.org/W1956090332","https://openalex.org/W1973754133","https://openalex.org/W1988393300","https://openalex.org/W1990061958","https://openalex.org/W1998300401","https://openalex.org/W2003967338","https://openalex.org/W2017200304","https://openalex.org/W2023863508","https://openalex.org/W2028903194","https://openalex.org/W2028904582","https://openalex.org/W2032231928","https://openalex.org/W2034206030","https://openalex.org/W2035588418","https://openalex.org/W2038555630","https://openalex.org/W2041726559","https://openalex.org/W2041754606","https://openalex.org/W2048869777","https://openalex.org/W2054984882","https://openalex.org/W2056002855","https://openalex.org/W2065718231","https://openalex.org/W2089026820","https://openalex.org/W2099316694","https://openalex.org/W2099357760","https://openalex.org/W2103081605","https://openalex.org/W2106304690","https://openalex.org/W2115273783","https://openalex.org/W2115772919","https://openalex.org/W2128091972","https://openalex.org/W2138247964","https://openalex.org/W2152893838","https://openalex.org/W2157907093","https://openalex.org/W2159588654","https://openalex.org/W2160609016","https://openalex.org/W2162665632","https://openalex.org/W2162891889","https://openalex.org/W2950063146","https://openalex.org/W4200351727","https://openalex.org/W4246105018"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2377079823","https://openalex.org/W2902352756","https://openalex.org/W2605676258","https://openalex.org/W2599962286","https://openalex.org/W2319582300"],"abstract_inverted_index":{"BACKGROUND:":[0],"Given":[1],"a":[2,99,157,215],"set":[3],"of":[4,29,89,107,120,181,218,232,240,263,266,277],"DNA":[5],"sequences":[6,130],"s1,":[7],"...,":[8],"st,":[9],"the":[10,30,66,71,76,105,108,112,136,142,150,168,178,187,207,230,238,243,251,267,275,278],"(l,":[11],"d)":[12],"motif":[13,20,67,113,280],"problem":[14,69,77],"is":[15,45,78,84,118,156,183,197,284,313],"to":[16,64,86,103,131,166,185,206,249,305],"find":[17,132],"an":[18],"l-length":[19],"sequence":[21,37],"M":[22],",":[23],"not":[24],"necessary":[25],"existing":[26,164,209],"in":[27,70,141,259],"any":[28,290],"input":[31],"sequences,":[32],"such":[33],"that":[34,195,229,300],"for":[35,111,315,317],"each":[36],"si,":[38],"1":[39],"\u2264":[40,42,128],"i":[41],"t,":[43],"there":[44,196],"at":[46,52,320],"least":[47],"one":[48],"subsequence":[49],"differing":[50],"with":[51,237],"most":[53],"d":[54],"mismatches":[55],"from":[56],"M.":[57],"Many":[58],"exact":[59,109,279],"algorithms":[60,110,165],"have":[61],"been":[62],"developed":[63,312],"solve":[65,250],"finding":[68,114],"last":[72],"three":[73],"decades.":[74],"However,":[75],"still":[79],"challenging":[80,254],"and":[81,91],"its":[82],"solution":[83,276],"limited":[85],"small":[87],"values":[88],"l":[90],"d.":[92],"RESULTS:":[93],"In":[94,172],"this":[95,173],"paper":[96],"we":[97,125,148,175,212,246,311],"present":[98,214],"new":[100,291],"efficient":[101],"method":[102,117,155,204,220,272,283,302],"improve":[104],"performance":[106,231],"problem.":[115,281],"Our":[116,154,191,226,271,282],"composed":[119],"two":[121],"main":[122],"steps:":[123],"First,":[124],"process":[126],"q":[127,182],"t":[129],"candidate":[133,137],"motifs.":[134,308],"Second,":[135],"motifs":[138],"are":[139],"searched":[140],"remaining":[143],"sequences.":[144],"For":[145],"both":[146],"steps,":[147],"use":[149],"best":[151,169,188,208],"available":[152,314],"algorithms.":[153],"hybrid":[158],"one,":[159],"because":[160,286],"it":[161,287],"integrates":[162],"currently":[163],"achieve":[167,186],"running":[170,189,221],"time.":[171,190],"paper,":[174],"show":[176,194,228],"how":[177],"optimal":[179],"value":[180],"determined":[184],"experimental":[192],"results":[193],"about":[198],"24%":[199],"speed-up":[200],"achieved":[201],"by":[202],"our":[203,219,233,301],"compared":[205],"algorithm.":[210],"Furthermore,":[211],"also":[213],"parallel":[216,244],"version":[217],"on":[222,295],"shared":[223],"memory":[224],"architecture.":[225],"experiments":[227],"algorithm":[234,293],"scales":[235],"linearly":[236],"number":[239],"processors.":[241],"Using":[242],"version,":[245],"were":[247],"able":[248],"(21,":[252],"8)":[253],"instance":[255],"using":[256],"8":[257],"processors":[258],"20.42":[260],"hours":[261],"instead":[262],"6.68":[264],"days":[265],"serial":[268],"version.":[269],"CONCLUSIONS:":[270],"speeds":[273],"up":[274],"generic,":[285],"can":[288],"accommodate":[289],"faster":[292],"based":[294],"traditional":[296],"methods.":[297],"We":[298],"expect":[299],"will":[303],"help":[304],"discover":[306],"longer":[307],"The":[309],"software":[310],"free":[316],"academic":[318],"research":[319],"http://www.nubios.nileu.edu.eg/tools/hymotif.":[321]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
