{"id":"https://openalex.org/W3004608784","doi":"https://doi.org/10.1109/bibm47256.2019.8983393","title":"SOF: An Efficient String Graph Construction Algorithm","display_name":"SOF: An Efficient String Graph Construction Algorithm","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004608784","doi":"https://doi.org/10.1109/bibm47256.2019.8983393","mag":"3004608784"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983393","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983393","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5025147780","display_name":"Md Sarowar Morshed","orcid":"https://orcid.org/0000-0002-9079-147X"},"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":"S. M. Iqbal Morshed","raw_affiliation_strings":["University of Central Florida,Department of Computer Science,Orlando,Florida,USA","Department of Computer Science, University of Central Florida, Orlando, Florida, USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida,Department of Computer Science,Orlando,Florida,USA","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"Department of Computer Science, University of Central Florida, Orlando, Florida, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015513138","display_name":"Shibu Yooseph","orcid":"https://orcid.org/0000-0001-5581-5002"},"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":"Shibu Yooseph","raw_affiliation_strings":["University of Central Florida,Genomics and Bioinformatics Cluster,Orlando,Florida,USA","Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, Florida, USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida,Genomics and Bioinformatics Cluster,Orlando,Florida,USA","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, Florida, USA","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5025147780"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":null,"apc_paid":null,"fwci":0.0852,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.48852332,"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":"283","last_page":"287"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9991000294685364,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9696000218391418,"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/de-bruijn-graph","display_name":"De Bruijn graph","score":0.7448571920394897},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6767191886901855},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.5557971596717834},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.48206669092178345},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.4794279932975769},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.472755491733551},{"id":"https://openalex.org/keywords/string-searching-algorithm","display_name":"String searching algorithm","score":0.4549540877342224},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.436794251203537},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.41576290130615234},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1668582558631897},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11482039093971252}],"concepts":[{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.7448571920394897},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6767191886901855},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.5557971596717834},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.48206669092178345},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.4794279932975769},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.472755491733551},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.4549540877342224},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.436794251203537},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.41576290130615234},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1668582558631897},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11482039093971252},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983393","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983393","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W9498632","https://openalex.org/W2023911006","https://openalex.org/W2074332603","https://openalex.org/W2107772251","https://openalex.org/W2115501618","https://openalex.org/W2121778970","https://openalex.org/W2136651963","https://openalex.org/W2153891971","https://openalex.org/W2156104322","https://openalex.org/W2159647614","https://openalex.org/W2161048357","https://openalex.org/W2301039091","https://openalex.org/W2537565528","https://openalex.org/W2734493815"],"related_works":["https://openalex.org/W1975912699","https://openalex.org/W2949604727","https://openalex.org/W2594227215","https://openalex.org/W2883795128","https://openalex.org/W2032875787","https://openalex.org/W2021626172","https://openalex.org/W2024445065","https://openalex.org/W2998410131","https://openalex.org/W2462428821","https://openalex.org/W4288309913"],"abstract_inverted_index":{"In":[0,94],"contrast":[1],"to":[2,17,78,117,183],"genome":[3,55,190],"assemblers":[4],"that":[5,130],"use":[6],"de":[7],"Bruijn":[8],"graphs,":[9],"those":[10],"based":[11],"on":[12],"string":[13,31,49,69,121,140,152],"graphs":[14],"are":[15],"able":[16],"losslessly":[18],"retain":[19],"information":[20],"from":[21,123],"sequence":[22,87],"data.":[23],"However,":[24],"despite":[25],"the":[26,42,65,79,109,139,149,158,165,173,184],"advantages":[27],"provided":[28,144,192],"by":[29,90],"a":[30,48,75,83,99,120,170,179],"graph":[32,50,70,122,141],"framework":[33],"in":[34,38,145,172,193],"repeat":[35],"detection":[36],"and":[37,103,114,186],"maintaining":[39,156],"read":[40],"coherence,":[41],"high":[43],"computational":[44],"cost":[45],"for":[46,54,68,81,189],"constructing":[47],"hinders":[51],"its":[52],"usability":[53],"assembly.":[56],"Even":[57],"though":[58],"different":[59],"algorithms":[60],"have":[61],"been":[62],"proposed":[63],"over":[64],"last":[66],"decade":[67],"construction,":[71],"efficiency":[72],"is":[73,132],"still":[74],"challenge":[76],"due":[77],"demand":[80],"processing":[82],"large":[84],"amount":[85],"of":[86,111,148,167],"data":[88],"generated":[89],"Next-Generation":[91],"Sequencing":[92],"technologies.":[93],"this":[95],"paper,":[96],"we":[97],"provide":[98],"novel,":[100],"linear":[101],"time":[102],"alphabet-size-independent":[104],"algorithm":[105,143],"SOF":[106,131,168],"which":[107],"uses":[108],"property":[110],"irreducible":[112],"edges":[113,116],"transitive":[115],"efficiently":[118],"construct":[119],"an":[124],"overlap":[125],"graph.":[126],"Experimental":[127],"results":[128],"show":[129],"at":[133],"least":[134],"2.3":[135],"times":[136],"faster":[137],"than":[138],"construction":[142],"SGA":[146,174],"(one":[147],"most":[150],"popular":[151],"graph-based":[153],"assemblers),":[154],"while":[155],"almost":[157],"same":[159],"memory":[160],"footprint":[161],"as":[162,169],"SGA.":[163,194],"Moreover,":[164],"implementation":[166],"subprogram":[171],"assembly":[175,191],"pipeline":[176],"will":[177],"allow":[178],"user":[180],"easy":[181],"access":[182],"preprocessing":[185],"postprocessing":[187],"steps":[188],"Implementation:":[195],"https://github.com/iqbalmorshed/sof.":[196]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
