{"id":"https://openalex.org/W4388127638","doi":"https://doi.org/10.3390/computation11110212","title":"Evaluating the Performance of Multiple Sequence Alignment Programs with Application to Genotyping SARS-CoV-2 in the Saudi Population","display_name":"Evaluating the Performance of Multiple Sequence Alignment Programs with Application to Genotyping SARS-CoV-2 in the Saudi Population","publication_year":2023,"publication_date":"2023-11-01","ids":{"openalex":"https://openalex.org/W4388127638","doi":"https://doi.org/10.3390/computation11110212"},"language":"en","primary_location":{"id":"doi:10.3390/computation11110212","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation11110212","pdf_url":"https://www.mdpi.com/2079-3197/11/11/212/pdf?version=1698826625","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2079-3197/11/11/212/pdf?version=1698826625","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103186378","display_name":"Aminah Alqahtani","orcid":"https://orcid.org/0009-0006-5376-6554"},"institutions":[{"id":"https://openalex.org/I240666556","display_name":"Imam Mohammad ibn Saud Islamic University","ror":"https://ror.org/05gxjyb39","country_code":"SA","type":"education","lineage":["https://openalex.org/I240666556"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Aminah Alqahtani","raw_affiliation_strings":["Computer Science Department, College of Computer and Information Sciences, Imam Mohammad Ibn Saud Islamic University, Riyadh 11564, Saudi Arabia"],"raw_orcid":"https://orcid.org/0009-0006-5376-6554","affiliations":[{"raw_affiliation_string":"Computer Science Department, College of Computer and Information Sciences, Imam Mohammad Ibn Saud Islamic University, Riyadh 11564, Saudi Arabia","institution_ids":["https://openalex.org/I240666556"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037893831","display_name":"Meznah Almutairy","orcid":"https://orcid.org/0000-0001-7254-1867"},"institutions":[{"id":"https://openalex.org/I240666556","display_name":"Imam Mohammad ibn Saud Islamic University","ror":"https://ror.org/05gxjyb39","country_code":"SA","type":"education","lineage":["https://openalex.org/I240666556"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Meznah Almutairy","raw_affiliation_strings":["Computer Science Department, College of Computer and Information Sciences, Imam Mohammad Ibn Saud Islamic University, Riyadh 11564, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0001-7254-1867","affiliations":[{"raw_affiliation_string":"Computer Science Department, College of Computer and Information Sciences, Imam Mohammad Ibn Saud Islamic University, Riyadh 11564, Saudi Arabia","institution_ids":["https://openalex.org/I240666556"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037893831"],"corresponding_institution_ids":["https://openalex.org/I240666556"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.7497,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.73283912,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"11","issue":"11","first_page":"212","last_page":"212"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976000189781189,"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":0.9976000189781189,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9973000288009644,"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"}},{"id":"https://openalex.org/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.6926326155662537},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5535866022109985},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.49756887555122375},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4829196631908417},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4806888997554779},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.47018444538116455},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.46200889348983765},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4449310004711151},{"id":"https://openalex.org/keywords/genetic-diversity","display_name":"Genetic diversity","score":0.4375249445438385},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43050479888916016},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.32249414920806885},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.27617740631103516},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1158204972743988},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09333276748657227}],"concepts":[{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.6926326155662537},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5535866022109985},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.49756887555122375},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4829196631908417},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4806888997554779},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.47018444538116455},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.46200889348983765},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4449310004711151},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.4375249445438385},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43050479888916016},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.32249414920806885},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.27617740631103516},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1158204972743988},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09333276748657227},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/computation11110212","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation11110212","pdf_url":"https://www.mdpi.com/2079-3197/11/11/212/pdf?version=1698826625","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:5b2ca1f546f548c0ac97f844cddb992c","is_oa":true,"landing_page_url":"https://doaj.org/article/5b2ca1f546f548c0ac97f844cddb992c","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computation, Vol 11, Iss 11, p 212 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/computation11110212","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation11110212","pdf_url":"https://www.mdpi.com/2079-3197/11/11/212/pdf?version=1698826625","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388127638.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1527244384","https://openalex.org/W1638450793","https://openalex.org/W2022349790","https://openalex.org/W2091617798","https://openalex.org/W2114850508","https://openalex.org/W2117477006","https://openalex.org/W2118716355","https://openalex.org/W2127322768","https://openalex.org/W2127774996","https://openalex.org/W2132926880","https://openalex.org/W2141637710","https://openalex.org/W2166637863","https://openalex.org/W2258865027","https://openalex.org/W2266687156","https://openalex.org/W2605343262","https://openalex.org/W2906852436","https://openalex.org/W2966929769","https://openalex.org/W3003217347","https://openalex.org/W3017703988","https://openalex.org/W3081851050","https://openalex.org/W3121460605","https://openalex.org/W3128334184","https://openalex.org/W3133723108","https://openalex.org/W3137049262","https://openalex.org/W4210851756"],"related_works":["https://openalex.org/W2378369506","https://openalex.org/W2030447374","https://openalex.org/W2353370357","https://openalex.org/W2806032235","https://openalex.org/W2755824586","https://openalex.org/W4280553679","https://openalex.org/W2377518790","https://openalex.org/W2394359576","https://openalex.org/W2463477745","https://openalex.org/W2349105149"],"abstract_inverted_index":{"This":[0],"study":[1],"explores":[2],"the":[3,20,26,35,78,86,94,133,143,175,187,197],"accuracy":[4,62],"and":[5,17,57,68,116,125,154],"efficiency":[6],"of":[7,22,49,73,80,121,167,184,199],"multiple":[8],"sequence":[9],"alignment":[10,95],"(MSA)":[11],"programs,":[12],"focusing":[13],"on":[14],"Clustal\u03a9,":[15],"MAFFT,":[16],"MUSCLE":[18,58,131],"in":[19,65,186,203],"context":[21],"genotyping":[23,74,110],"SARS-CoV-2":[24,87,156],"for":[25,42],"Saudi":[27,153,188],"population.":[28,176],"Our":[29],"results":[30],"indicate":[31],"that":[32,55,77,98],"MAFFT":[33,56,126,141],"outperforms":[34],"others,":[36],"making":[37],"it":[38],"an":[39],"ideal":[40],"choice":[41],"large-scale":[43],"genomic":[44],"analyses.":[45,205],"The":[46,71],"comparative":[47],"performance":[48],"MSAs":[50],"assembled":[51],"using":[52,99],"MergeAlign":[53],"demonstrates":[54],"consistently":[59,164],"exhibit":[60,163],"higher":[61,165,182],"than":[63],"Clustal\u03a9":[64,124],"both":[66],"reference-based":[67],"consensus-based":[69],"approaches.":[70],"evaluation":[72],"effectiveness":[75],"reveals":[76,180],"addition":[79],"a":[81,181],"reference":[82],"sequence,":[83],"such":[84],"as":[85,142],"Wuhan-Hu-1":[88],"isolate,":[89],"does":[90],"not":[91],"significantly":[92],"affect":[93],"process,":[96],"suggesting":[97,190],"consensus":[100],"sequences":[101],"derived":[102],"from":[103],"individual":[104],"MSA":[105,122,146],"alignments":[106],"may":[107],"yield":[108],"comparable":[109],"outcomes.":[111],"Investigating":[112],"single-nucleotide":[113],"polymorphisms":[114],"(SNPs)":[115],"mutations":[117],"highlights":[118],"distinctive":[119],"features":[120],"programs.":[123],"show":[127],"similar":[128],"counts,":[129],"while":[130],"displays":[132],"highest":[134],"SNP":[135,138],"count.":[136],"High-frequency":[137],"analysis":[139,179],"identifies":[140],"most":[144],"accurate":[145],"program,":[147],"emphasizing":[148],"its":[149],"reliability.":[150],"Comparisons":[151],"between":[152],"global":[155],"populations":[157],"underscore":[158],"regional":[159,201],"genetic":[160,172,204],"variations.":[161],"Saudis":[162],"frequencies":[166],"high-frequency":[168],"SNPs,":[169],"attributed":[170],"to":[171],"similarity":[173],"within":[174],"Transmission":[177],"dynamics":[178],"frequency":[183],"co-mutations":[185],"dataset,":[189],"shared":[191],"evolutionary":[192],"patterns.":[193],"These":[194],"findings":[195],"emphasize":[196],"importance":[198],"considering":[200],"diversity":[202]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-01-23T23:20:30.427331","created_date":"2025-10-10T00:00:00"}
