{"id":"https://openalex.org/W2562002492","doi":"https://doi.org/10.1186/s12859-016-1365-2","title":"A fast exact sequential algorithm for the partial digest problem","display_name":"A fast exact sequential algorithm for the partial digest problem","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2562002492","doi":"https://doi.org/10.1186/s12859-016-1365-2","mag":"2562002492","pmid":"https://pubmed.ncbi.nlm.nih.gov/28155644"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1365-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1365-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1365-2","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/track/pdf/10.1186/s12859-016-1365-2","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/I4210144839","display_name":"Hamad bin Khalifa University","ror":"https://ror.org/03eyq4y97","country_code":"QA","type":"education","lineage":["https://openalex.org/I4210144839"]}],"countries":["QA"],"is_corresponding":true,"raw_author_name":"Mostafa M. Abbas","raw_affiliation_strings":["Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar. mohamza@hbku.edu.qa","Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar. mohamza@hbku.edu.qa","institution_ids":["https://openalex.org/I4210144839"]},{"raw_affiliation_string":"Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar","institution_ids":["https://openalex.org/I4210144839"]}]},{"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":true,"raw_author_name":"Hazem M. Bahig","raw_affiliation_strings":["Computer Science Division, Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt. hazem.m.bahig@gmail.com","Computer Science Division, Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Division, Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt. hazem.m.bahig@gmail.com","institution_ids":["https://openalex.org/I107720978"]},{"raw_affiliation_string":"Computer Science Division, Department of Mathematics, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt","institution_ids":["https://openalex.org/I107720978"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5024925431","https://openalex.org/A5052114281"],"corresponding_institution_ids":["https://openalex.org/I107720978","https://openalex.org/I4210144839"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.3662,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.84740536,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"17","issue":"S19","first_page":"510","last_page":"510"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.8575999736785889,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.8575999736785889,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0272000003606081,"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/T12029","display_name":"DNA and Biological Computing","score":0.018799999728798866,"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/algorithm","display_name":"Algorithm","score":0.7244063019752502},{"id":"https://openalex.org/keywords/traverse","display_name":"Traverse","score":0.6366556286811829},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5500631332397461},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44022294878959656},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4155372679233551},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3036033809185028},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.08948269486427307}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7244063019752502},{"id":"https://openalex.org/C176809094","wikidata":"https://www.wikidata.org/wiki/Q15401496","display_name":"Traverse","level":2,"score":0.6366556286811829},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5500631332397461},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44022294878959656},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4155372679233551},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3036033809185028},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08948269486427307},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004269","descriptor_name":"DNA, Bacterial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008156","descriptor_name":"Luciferases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008156","descriptor_name":"Luciferases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008156","descriptor_name":"Luciferases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-016-1365-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1365-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1365-2","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:28155644","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28155644","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:figshare.com:article/27094639","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/A_fast_exact_sequential_algorithm_for_the_partial_digest_problem/27094639","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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"},{"id":"pmh:oai:pubmedcentral.nih.gov:5259970","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5259970","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-1365-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1365-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1365-2","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":[{"id":"https://openalex.org/F4320309815","display_name":"Qatar Foundation","ror":"https://ror.org/01cawbq05"},{"id":"https://openalex.org/F4320319188","display_name":"Hamad Bin Khalifa University","ror":"https://ror.org/03eyq4y97"},{"id":"https://openalex.org/F4320322334","display_name":"Khalifa University of Science, Technology and Research","ror":"https://ror.org/05hffr360"},{"id":"https://openalex.org/F4320322472","display_name":"Qatar University","ror":"https://ror.org/00yhnba62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2562002492.pdf","grobid_xml":"https://content.openalex.org/works/W2562002492.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W327613181","https://openalex.org/W1482500017","https://openalex.org/W1543636183","https://openalex.org/W1583866884","https://openalex.org/W1865467296","https://openalex.org/W1881549354","https://openalex.org/W1909392995","https://openalex.org/W1996453271","https://openalex.org/W2003389942","https://openalex.org/W2017181565","https://openalex.org/W2019143745","https://openalex.org/W2021134019","https://openalex.org/W2036145194","https://openalex.org/W2039327326","https://openalex.org/W2053840591","https://openalex.org/W2063444955","https://openalex.org/W2081766760","https://openalex.org/W2108848024","https://openalex.org/W2135742714","https://openalex.org/W2144634347","https://openalex.org/W2148831358","https://openalex.org/W2153025396","https://openalex.org/W2158787071","https://openalex.org/W2280527731","https://openalex.org/W2314225431","https://openalex.org/W3022371179","https://openalex.org/W4230574484","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2354594976","https://openalex.org/W2384786133","https://openalex.org/W1588720508","https://openalex.org/W1571601326","https://openalex.org/W2368623353","https://openalex.org/W2366803732","https://openalex.org/W2366394613","https://openalex.org/W2538870524","https://openalex.org/W2371244664","https://openalex.org/W2121551448"],"abstract_inverted_index":{"BACKGROUND:":[0],"Restriction":[1],"site":[2],"analysis":[3],"involves":[4],"determining":[5],"the":[6,12,22,25,48,62,68,84,88,102,108,135,138,143,149,153,167,171,184,190,204,211],"locations":[7,50],"of":[8,14,24,51,125,137,177,196],"restriction":[9,52],"sites":[10,53],"after":[11],"process":[13],"digestion":[15,57],"by":[16,106],"reconstructing":[17],"their":[18],"positions":[19],"based":[20],"on":[21],"lengths":[23],"cut":[26,37],"DNA.":[27],"Using":[28],"different":[29],"reaction":[30],"times":[31],"with":[32,67,111],"a":[33,40,44,55,112,162,207],"single":[34],"enzyme":[35],"to":[36,61,82,96,133,145,165,202],"DNA":[38],"is":[39,58,94,161,179,200,216],"technique":[41],"known":[42,70,186,213],"as":[43],"partial":[45,56,89,172],"digestion.":[46],"Determining":[47],"exact":[49,85,168],"following":[54],"challenging":[59],"due":[60],"computational":[63],"time":[64],"required":[65],"even":[66],"best":[69,185,212],"practical":[71,187,214],"algorithm.":[72,139],"RESULTS:":[73],"In":[74],"this":[75],"paper,":[76],"we":[77],"introduce":[78],"an":[79],"efficient":[80],"algorithm":[81,93,144,160,188,199,215],"find":[83,97,166],"solution":[86,109,169],"for":[87,101,148,170,189],"digest":[90,173],"problem.":[91,174],"The":[92,175],"able":[95,201],"all":[98,120],"possible":[99],"solutions":[100],"input":[103],"and":[104,118,129,152],"works":[105],"traversing":[107],"tree":[110],"breadth-first":[113],"search":[114],"in":[115,206],"two":[116],"stages":[117],"deleting":[119],"repeated":[121],"subproblems.":[122],"Two":[123],"types":[124],"simulated":[126],"data,":[127],"random":[128],"Zhang,":[130],"are":[131],"used":[132],"measure":[134],"efficiency":[136],"We":[140],"also":[141],"apply":[142],"real":[146],"data":[147],"Luciferase":[150],"gene":[151],"E.":[154],"coli":[155],"K12":[156],"genome.":[157],"CONCLUSION:":[158],"Our":[159],"fast":[163],"tool":[164],"percentage":[176],"improvement":[178],"more":[180],"than":[181],"75%":[182],"over":[183],"worst":[191],"case.":[192],"For":[193],"large":[194],"numbers":[195],"inputs,":[197],"our":[198],"solve":[203],"problem":[205],"suitable":[208],"time,":[209],"while":[210],"unable.":[217]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
