{"id":"https://openalex.org/W2557279061","doi":"https://doi.org/10.1145/2975167.2985659","title":"Adaptive Local Realignment via Parameter Advising","display_name":"Adaptive Local Realignment via Parameter Advising","publication_year":2016,"publication_date":"2016-10-02","ids":{"openalex":"https://openalex.org/W2557279061","doi":"https://doi.org/10.1145/2975167.2985659","mag":"2557279061"},"language":"en","primary_location":{"id":"doi:10.1145/2975167.2985659","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2975167.2985659","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=2985659&type=pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"http://dl.acm.org/ft_gateway.cfm?id=2985659&type=pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014004628","display_name":"Dan DeBlasio","orcid":"https://orcid.org/0000-0003-4110-4431"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dan DeBlasio","raw_affiliation_strings":["Department of Computer Science, University of Arizona, Tucson, Arizona USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Arizona, Tucson, Arizona USA","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083998316","display_name":"John Kececioglu","orcid":"https://orcid.org/0000-0003-1204-6535"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Kececioglu","raw_affiliation_strings":["Department of Computer Science, University of Arizona, Tucson, Arizona USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Arizona, Tucson, Arizona USA","institution_ids":["https://openalex.org/I138006243"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5014004628"],"corresponding_institution_ids":["https://openalex.org/I138006243"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09445865,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"510","last_page":"511"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9891999959945679,"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/sequence","display_name":"Sequence (biology)","score":0.6698260307312012},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.596255898475647},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5686038732528687},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4189727008342743},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22578251361846924},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17727655172348022},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07269150018692017}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6698260307312012},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.596255898475647},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5686038732528687},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4189727008342743},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22578251361846924},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17727655172348022},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07269150018692017}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2975167.2985659","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2975167.2985659","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=2985659&type=pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/2975167.2985659","is_oa":true,"landing_page_url":"https://doi.org/10.1145/2975167.2985659","pdf_url":"http://dl.acm.org/ft_gateway.cfm?id=2985659&type=pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2375335175","display_name":null,"funder_award_id":"IIS-1217886","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2557279061.pdf","grobid_xml":"https://content.openalex.org/works/W2557279061.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W2007924998","https://openalex.org/W2566074425"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Mutation":[0],"rates":[1],"can":[2],"vary":[3],"across":[4,36,80],"the":[5,20,26,43,64,81],"residues":[6],"of":[7,23,63,83],"a":[8,46,84],"protein,":[9],"but":[10],"when":[11,67],"multiple":[12,70],"sequence":[13,71],"alignments":[14],"are":[15],"computed":[16],"for":[17,25,42],"protein":[18,69,85],"sequences,":[19],"same":[21],"choice":[22],"values":[24],"substitution":[27],"score":[28],"and":[29],"gap":[30],"penalty":[31],"parameters":[32],"is":[33],"often":[34],"used":[35],"their":[37],"entire":[38],"length.":[39],"We":[40],"provide":[41],"first":[44],"time":[45],"new":[47],"method":[48],"called":[49],"adaptive":[50],"local":[51],"realignment":[52],"that":[53],"automatically":[54],"uses":[55],"diverse":[56],"alignment":[57],"parameter":[58,75],"settings":[59,76],"in":[60],"different":[61],"regions":[62],"input":[65],"sequences":[66],"computing":[68],"alignments.":[72],"This":[73],"allows":[74],"to":[77,86],"locally":[78],"adapt":[79],"length":[82],"more":[87],"closely":[88],"match":[89],"varying":[90],"mutation":[91],"rates.":[92]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}