{"id":"https://openalex.org/W2900729913","doi":"https://doi.org/10.1109/iccabs.2018.8542085","title":"Codon-Based Sequence Alignment for Mutation Analysis by High-Throughput Sequencing","display_name":"Codon-Based Sequence Alignment for Mutation Analysis by High-Throughput Sequencing","publication_year":2018,"publication_date":"2018-10-01","ids":{"openalex":"https://openalex.org/W2900729913","doi":"https://doi.org/10.1109/iccabs.2018.8542085","mag":"2900729913"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2018.8542085","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2018.8542085","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"type":"conference-abstract","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/A5107809749","display_name":"Sing\u2010Hoi Sze","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sing-Hoi Sze","raw_affiliation_strings":["Department of Computer Science and Engineering, Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029585326","display_name":"Craig D. Kaplan","orcid":"https://orcid.org/0000-0002-7518-695X"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Craig D. Kaplan","raw_affiliation_strings":["Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I91045830"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9984999895095825,"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":0.9754999876022339,"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/indel","display_name":"Indel","score":0.7256900072097778},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.5807310342788696},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5785916447639465},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.5773757696151733},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5336293578147888},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5203537344932556},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5046740770339966},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4598153233528137},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4574941098690033},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4514178931713104},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4433874189853668},{"id":"https://openalex.org/keywords/start-codon","display_name":"Start codon","score":0.4404069781303406},{"id":"https://openalex.org/keywords/codon-usage-bias","display_name":"Codon usage bias","score":0.4227634072303772},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.41927406191825867},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.40117472410202026},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3993460536003113},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32719993591308594},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.32147976756095886},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.25434184074401855},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20763033628463745},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.15738838911056519},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.14976581931114197}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.7256900072097778},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.5807310342788696},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5785916447639465},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.5773757696151733},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5336293578147888},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5203537344932556},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5046740770339966},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4598153233528137},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4574941098690033},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4514178931713104},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4433874189853668},{"id":"https://openalex.org/C176990463","wikidata":"https://www.wikidata.org/wiki/Q1854186","display_name":"Start codon","level":4,"score":0.4404069781303406},{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.4227634072303772},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.41927406191825867},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.40117472410202026},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3993460536003113},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32719993591308594},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.32147976756095886},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.25434184074401855},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20763033628463745},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.15738838911056519},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.14976581931114197},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/iccabs.2018.8542085","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2018.8542085","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2044364290","https://openalex.org/W2730968108","https://openalex.org/W4386770652","https://openalex.org/W1482324242","https://openalex.org/W2122131968","https://openalex.org/W2759306076","https://openalex.org/W1886146948","https://openalex.org/W187239587","https://openalex.org/W1615242748"],"abstract_inverted_index":{"The":[0],"advance":[1],"of":[2,24,75,88,104,146],"high-throughput":[3,156],"sequencing":[4,157],"has":[5,128],"made":[6,191],"it":[7],"possible":[8],"to":[9,34,38,142,170,184],"perform":[10],"large-scale":[11],"mutation":[12],"analysis":[13],"by":[14,64],"altering":[15],"codons":[16],"on":[17],"a":[18,59,79,83,86,94,98,113],"sequence":[19,28,61],"and":[20,101],"investigating":[21],"the":[22,25,36,39,55,66,129,134,144,149,171],"effect":[23,145],"changes.":[26],"While":[27],"alignment":[29,47,62],"algorithms":[30],"can":[31],"be":[32,190],"applied":[33],"compare":[35,167],"reads":[37],"original":[40],"unaltered":[41],"sequence,":[42],"neither":[43],"nucleotide-based":[44,135,175,193],"nor":[45],"protein-based":[46],"is":[48,81,96,111,182],"completely":[49],"suitable":[50],"for":[51],"analyzing":[52],"changes":[53],"at":[54,89],"codon":[56,80,95,125],"level.We":[57],"develop":[58],"codon-based":[60],"algorithm":[63,141,181],"modifying":[65],"dynamic":[67,136],"programming":[68,137],"equations":[69],"so":[70],"that":[71,159,179,188],"an":[72,102],"exact":[73],"match":[74],"three":[76,109],"letters":[77,110],"in":[78,93,163],"assigned":[82,97,112],"positive":[84],"score,":[85,100],"mismatch":[87],"least":[90],"one":[91],"letter":[92],"negative":[99,115],"indel":[103],"either":[105],"one,":[106],"two":[107],"or":[108],"constant":[114],"score.":[116],"This":[117],"strategy":[118],"models":[119],"what":[120],"could":[121,189],"happen":[122],"within":[123,148],"each":[124],"directly.":[126],"It":[127],"same":[130],"time":[131],"complexity":[132],"as":[133],"algorithm.We":[138],"apply":[139],"our":[140,164,168,180],"analyze":[143],"mutations":[147],"RNA":[150],"Polymerase":[151],"II":[152],"trigger":[153],"loop":[154],"from":[155],"libraries":[158],"we":[160],"have":[161],"generated":[162],"lab.":[165],"We":[166,177],"results":[169],"ones":[172],"obtained":[173],"with":[174,192],"alignment.":[176,194],"show":[178],"able":[183],"avoid":[185],"systematic":[186],"errors":[187]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
