{"id":"https://openalex.org/W1981549363","doi":"https://doi.org/10.4304/jsw.9.10.2622-2627","title":"Memory Optimization for Global Protein Network Alignment Using Pushdown Automata and De Bruijn Graph","display_name":"Memory Optimization for Global Protein Network Alignment Using Pushdown Automata and De Bruijn Graph","publication_year":2014,"publication_date":"2014-10-01","ids":{"openalex":"https://openalex.org/W1981549363","doi":"https://doi.org/10.4304/jsw.9.10.2622-2627","mag":"1981549363"},"language":"en","primary_location":{"id":"doi:10.4304/jsw.9.10.2622-2627","is_oa":false,"landing_page_url":"https://doi.org/10.4304/jsw.9.10.2622-2627","pdf_url":null,"source":{"id":"https://openalex.org/S114141714","display_name":"Journal of Software","issn_l":"1796-217X","issn":["1796-217X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318660","host_organization_name":"Academy Publisher","host_organization_lineage":["https://openalex.org/P4310318660"],"host_organization_lineage_names":["Academy Publisher"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Software","raw_type":"journal-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/A5062177671","display_name":"Md. Sarwar Kamal","orcid":"https://orcid.org/0000-0002-1945-821X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sarwar Kamal","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5064264181","display_name":"Mohammad Ibrahim Khan","orcid":"https://orcid.org/0000-0002-4228-6727"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mohammad Ibrahim Khan","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062177671"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1394,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.51882014,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"9","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9950000047683716,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9950000047683716,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9890999794006348,"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/T11269","display_name":"Algorithms and Data Compression","score":0.984000027179718,"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/computer-science","display_name":"Computer science","score":0.9108203649520874},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.6477283239364624},{"id":"https://openalex.org/keywords/pushdown-automaton","display_name":"Pushdown automaton","score":0.469830721616745},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4411023259162903},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4100510776042938},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.32923269271850586},{"id":"https://openalex.org/keywords/automaton","display_name":"Automaton","score":0.27665239572525024},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.0695919394493103}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.9108203649520874},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.6477283239364624},{"id":"https://openalex.org/C77944639","wikidata":"https://www.wikidata.org/wiki/Q751443","display_name":"Pushdown automaton","level":3,"score":0.469830721616745},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4411023259162903},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4100510776042938},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.32923269271850586},{"id":"https://openalex.org/C112505250","wikidata":"https://www.wikidata.org/wiki/Q787116","display_name":"Automaton","level":2,"score":0.27665239572525024},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.0695919394493103},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.4304/jsw.9.10.2622-2627","is_oa":false,"landing_page_url":"https://doi.org/10.4304/jsw.9.10.2622-2627","pdf_url":null,"source":{"id":"https://openalex.org/S114141714","display_name":"Journal of Software","issn_l":"1796-217X","issn":["1796-217X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318660","host_organization_name":"Academy Publisher","host_organization_lineage":["https://openalex.org/P4310318660"],"host_organization_lineage_names":["Academy Publisher"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Software","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1532744586","https://openalex.org/W1966822396","https://openalex.org/W2009119978","https://openalex.org/W2010361633","https://openalex.org/W2022910024","https://openalex.org/W2047665315","https://openalex.org/W2103635790","https://openalex.org/W2107427454","https://openalex.org/W2113915152","https://openalex.org/W2122961704","https://openalex.org/W2126419817","https://openalex.org/W2133531097","https://openalex.org/W2153124929","https://openalex.org/W2156660460","https://openalex.org/W2160648174","https://openalex.org/W2161546116","https://openalex.org/W2166524953","https://openalex.org/W6682963947"],"related_works":["https://openalex.org/W3198016531","https://openalex.org/W127787461","https://openalex.org/W2039773446","https://openalex.org/W1998517951","https://openalex.org/W2126473010","https://openalex.org/W2397939707","https://openalex.org/W4301429973","https://openalex.org/W2951695076","https://openalex.org/W2122316710","https://openalex.org/W1964377951"],"abstract_inverted_index":{"Ongoing":[0],"improvements":[1],"in":[2,108,144,177,189],"Computational":[3],"Biology":[4],"(CB)":[5],"research":[6],"have":[7,59,82,136],"generated":[8],"massive":[9],"amounts":[10],"of":[11,22,31,42,71,168,193],"Protein-Protein":[12],"Interactions":[13,77],"(PPIs)":[14,78],"data":[15,24,44,79,116,171],"set.":[16,80,117],"In":[17],"this":[18],"regards,":[19],"the":[20,29,69,84,123,181],"availability":[21],"PPI":[23],"for":[25,34,74,97,113],"several":[26,57],"organisms":[27],"provoke":[28],"discovery":[30],"computational":[32],"methods":[33,58],"measurements,":[35],"analysis,":[36],"modeling,":[37],"comparisons,":[38],"clustering":[39],"and":[40,53,90,127],"alignments":[41],"biological":[43],"networks.":[45],"Nevertheless,":[46],"fixed":[47],"network":[48,100],"comparison":[49],"is":[50,64,105],"computationally":[51],"stubborn":[52],"as":[54],"a":[55],"result":[56,156],"been":[60],"used":[61,107],"instead.\u00a0":[62],"It":[63],"very":[65],"crucial":[66],"to":[67,132],"utilize":[68],"memory":[70,85,145,176,192],"computing":[72],"devices":[73],"Protein-":[75],"Protein":[76],"We":[81,135],"compared":[83],"uses":[86],"using":[87],"Pushdown":[88,128,139,184],"Automata":[89,140],"de":[91,165],"Bruijn":[92,103],"graph":[93,104],"based":[94],"Bloom":[95,125,142,153,159],"Filter":[96],"global":[98],"proteins":[99],"alignment.\u00a0":[101],"De":[102,118],"regularly":[106],"Next":[109],"Generation":[110],"Sequencing":[111],"(NGS)":[112],"large":[114],"scale":[115],"novo":[119,166],"genome":[120,170],"assembler":[121],"utilizes":[122],"memory.":[124,134],"filter":[126,143,160],"Automat":[129,185],"perform":[130],"better":[131],"reduce":[133],"noticed":[137],"that":[138,158],"outperform":[141],"saving":[146],"but":[147],"it":[148],"takes":[149],"more":[150],"time":[151],"than":[152],"filter.":[154],"The":[155],"shows":[157],"software":[161],"Mania":[162],"implements":[163],"full":[164],"assembly":[167],"human":[169],"set":[172],"using\u00a0":[173],"6.5":[174],"GB":[175,191],"27":[178],"hours,":[179],"on":[180],"other":[182],"hand":[183],"performs":[186],"same":[187],"results":[188],"1":[190],"31":[194],"hours.":[195]},"counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
