{"id":"https://openalex.org/W2146712012","doi":"https://doi.org/10.1186/1471-2105-16-s2-a3","title":"Parameter advising for multiple sequence alignment","display_name":"Parameter advising for multiple sequence alignment","publication_year":2015,"publication_date":"2015-01-28","ids":{"openalex":"https://openalex.org/W2146712012","doi":"https://doi.org/10.1186/1471-2105-16-s2-a3","mag":"2146712012"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-16-s2-a3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s2-a3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S2-A3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S2-A3","any_repository_has_fulltext":true},"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, AZ, 85721, USA","Department of Computer Science, University of Arizona Tucson, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Arizona, Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"Department of Computer Science, University of Arizona Tucson, 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, AZ, 85721, USA","Department of Computer Science, University of Arizona Tucson, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Arizona, Tucson, AZ, 85721, USA","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"Department of Computer Science, University of Arizona Tucson, 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":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0563,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.77016395,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"16","issue":"S2","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":0.989300012588501,"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":0.989300012588501,"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":0.9847000241279602,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9836999773979187,"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/estimator","display_name":"Estimator","score":0.7686307430267334},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.678070068359375},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6459541320800781},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.6156835556030273},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5563576817512512},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.551727294921875},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.5003015995025635},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4036862254142761},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37898126244544983},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36864030361175537},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3362882733345032},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.19906887412071228}],"concepts":[{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.7686307430267334},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.678070068359375},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6459541320800781},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.6156835556030273},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5563576817512512},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.551727294921875},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.5003015995025635},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4036862254142761},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37898126244544983},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36864030361175537},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3362882733345032},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.19906887412071228},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-16-s2-a3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s2-a3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S2-A3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:repository.arizona.edu:10150/612932","is_oa":false,"landing_page_url":"http://hdl.handle.net/10150/612932","pdf_url":null,"source":{"id":"https://openalex.org/S4306400271","display_name":"UA Campus Repository (The University of Arizona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138006243","host_organization_name":"University of Arizona","host_organization_lineage":["https://openalex.org/I138006243"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Electronic Dissertation"},{"id":"pmh:oai:cds.cern.ch:2698619","is_oa":false,"landing_page_url":"http://cds.cern.ch/record/2698619","pdf_url":null,"source":{"id":"https://openalex.org/S4306402195","display_name":"CERN Document Server (European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:pubmedcentral.nih.gov:4340123","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4340123","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-16-s2-a3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s2-a3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S2-A3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6499999761581421,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2146712012.pdf","grobid_xml":"https://content.openalex.org/works/W2146712012.grobid-xml"},"referenced_works_count":99,"referenced_works":["https://openalex.org/W171034855","https://openalex.org/W605727707","https://openalex.org/W1507039213","https://openalex.org/W1519266993","https://openalex.org/W1567621547","https://openalex.org/W1590146311","https://openalex.org/W1590240800","https://openalex.org/W1646393397","https://openalex.org/W1694876563","https://openalex.org/W1844951369","https://openalex.org/W1870852322","https://openalex.org/W1963957860","https://openalex.org/W1964056758","https://openalex.org/W1969153299","https://openalex.org/W1974326986","https://openalex.org/W1981014117","https://openalex.org/W1989119850","https://openalex.org/W1990061958","https://openalex.org/W1991330646","https://openalex.org/W1993414412","https://openalex.org/W1994815346","https://openalex.org/W2003967338","https://openalex.org/W2007924998","https://openalex.org/W2009570821","https://openalex.org/W2011039300","https://openalex.org/W2011289056","https://openalex.org/W2021883973","https://openalex.org/W2022349790","https://openalex.org/W2030750720","https://openalex.org/W2033491972","https://openalex.org/W2035594133","https://openalex.org/W2055043387","https://openalex.org/W2060791849","https://openalex.org/W2068083406","https://openalex.org/W2068448872","https://openalex.org/W2073234837","https://openalex.org/W2074231493","https://openalex.org/W2074830661","https://openalex.org/W2075451741","https://openalex.org/W2076048958","https://openalex.org/W2085292202","https://openalex.org/W2094519647","https://openalex.org/W2096234003","https://openalex.org/W2097059553","https://openalex.org/W2097818324","https://openalex.org/W2101251774","https://openalex.org/W2101969356","https://openalex.org/W2102502076","https://openalex.org/W2102885074","https://openalex.org/W2105006906","https://openalex.org/W2106053110","https://openalex.org/W2106882534","https://openalex.org/W2107029482","https://openalex.org/W2108491719","https://openalex.org/W2110919845","https://openalex.org/W2111551123","https://openalex.org/W2114320077","https://openalex.org/W2114616367","https://openalex.org/W2115888213","https://openalex.org/W2117477006","https://openalex.org/W2120866529","https://openalex.org/W2121691652","https://openalex.org/W2122097054","https://openalex.org/W2123933470","https://openalex.org/W2127322768","https://openalex.org/W2127556561","https://openalex.org/W2127774996","https://openalex.org/W2130479394","https://openalex.org/W2130625618","https://openalex.org/W2132926880","https://openalex.org/W2133296809","https://openalex.org/W2138369959","https://openalex.org/W2140872496","https://openalex.org/W2140890018","https://openalex.org/W2141885858","https://openalex.org/W2142113273","https://openalex.org/W2143210482","https://openalex.org/W2143292980","https://openalex.org/W2143357251","https://openalex.org/W2144362290","https://openalex.org/W2147461064","https://openalex.org/W2148311769","https://openalex.org/W2150326938","https://openalex.org/W2151904894","https://openalex.org/W2153187042","https://openalex.org/W2154036437","https://openalex.org/W2154085147","https://openalex.org/W2154139219","https://openalex.org/W2155320525","https://openalex.org/W2160910042","https://openalex.org/W2161062388","https://openalex.org/W2166718648","https://openalex.org/W2169602699","https://openalex.org/W2170157200","https://openalex.org/W2181948338","https://openalex.org/W2523931589","https://openalex.org/W4205911826","https://openalex.org/W4252684946","https://openalex.org/W6732994188"],"related_works":["https://openalex.org/W4287880334","https://openalex.org/W4366700029","https://openalex.org/W4285230481","https://openalex.org/W4385769873","https://openalex.org/W2015759683","https://openalex.org/W4281634296","https://openalex.org/W4319161863","https://openalex.org/W2371687270","https://openalex.org/W4307819175","https://openalex.org/W2898674639"],"abstract_inverted_index":{"The":[0],"problem":[1,19,29],"of":[2,17,27,57,64,76,143,168,242,270,338,360,379],"aligning":[3],"multiple":[4,38],"protein":[5],"sequences":[6,136,363],"is":[7,54,94,183,194,208,286],"essential":[8],"to":[9,23,116,174,185,198,327,340,351,368,370],"many":[10,36],"biological":[11],"analyses,":[12],"but":[13,98],"most":[14],"standard":[15],"formulations":[16],"the":[18,25,28,74,77,84,91,105,134,149,153,175,190,284,293,314,332,343,361,377,380],"are":[20,35,172,248],"NP-complete.":[21],"Due":[22],"both":[24,342],"difficulty":[26],"and":[30,70,146,177,211,345,349],"its":[31,346],"practical":[32],"importance,":[33],"there":[34],"heuristic":[37],"sequence":[39],"aligners":[40,339],"that":[41,51,55,66,88,121,171,182,223,233],"a":[42,62,101,118,123,141,199,205,219,239,252,271,275,308,336],"researcher":[43],"has":[44,61,160],"at":[45],"their":[46],"disposal.":[47],"A":[48,130,157],"basic":[49],"issue":[50],"frequently":[52],"arises":[53],"each":[56,127,138,289],"these":[58],"alignment":[59,78,103,125,151,207],"tools":[60],"multitude":[63],"parameters":[65],"must":[67],"be":[68],"set,":[69],"which":[71,93,330,355],"greatly":[72],"affect":[73],"quality":[75],"produced.":[79,156],"Most":[80],"users":[81],"rely":[82],"on":[83,96,335],"default":[85,310],"parameter":[86,114,119,131,144,158,169,290,298,311,321,347,366],"setting":[87,120],"comes":[89],"with":[90,196,364],"aligner,":[92,176],"optimal":[95],"average,":[97],"can":[99,213,356],"produce":[100],"low-quality":[102],"for":[104,126,137,229,265,274,288,297,313],"given":[106,128,173,272],"inputs.":[107],"This":[108,317],"dissertation":[109,318],"develops":[110],"an":[111,165,179,235,261,267],"approach":[112],"called":[113,226],"advising":[115,299,301,322,333],"find":[117],"produces":[122],"high-quality":[124],"input.":[129],"advisor":[132,159,166,268],"aligns":[133],"input":[135,362],"choice":[139,291,312],"in":[140,203,292,323],"collection":[142,337],"settings,":[145,348],"then":[147],"selects":[148],"best":[150],"from":[152],"resulting":[154],"alignments":[155,187],"two":[161,324],"major":[162],"components:":[163],"(i)":[164,326],"set":[167,269],"choices":[170,367],"(ii)":[178,350],"accuracy":[180,193,221,231,236,302],"estimator":[181,222],"used":[184],"rank":[186],"produced":[188],"by":[189,250,303],"aligner.":[191],"Alignment":[192],"measured":[195],"respect":[197],"known":[200],"reference":[201,206],"alignment,":[202,329],"practice":[204],"not":[209],"available,":[210],"we":[212,224],"only":[214],"estimate":[215,237],"accuracy.":[216],"We":[217,258],"develop":[218,260],"new":[220],"call":[225],"Facet":[227,296],"(short":[228],"\"feature-based":[230],"estimator\")":[232],"computes":[234],"as":[238,283,373],"linear":[240,255],"combination":[241],"efficiently-computable":[243],"feature":[244],"functions,":[245],"whose":[246,278],"coefficients":[247],"learned":[249],"solving":[251],"large":[253],"scale":[254],"programming":[256],"problem.":[257],"also":[259],"efficient":[262],"approximation":[263],"algorithm":[264],"finding":[266],"cardinality":[273,279],"fixed":[276],"estimator,":[277],"should":[280],"ideally":[281],"small,":[282],"aligner":[285,344],"invoked":[287],"set.":[294],"Using":[295],"boosts":[300],"almost":[304],"20%":[305],"beyond":[306],"using":[307],"single":[309],"hardest-to-align":[315],"benchmarks.":[316],"further":[319],"applies":[320],"ways:":[325],"ensemble":[328],"uses":[331],"process":[334],"choose":[341],"adaptive":[352],"local":[353],"realignment,":[354],"align":[357],"different":[358],"regions":[359],"distinct":[365],"conform":[369],"mutation":[371],"rates":[372],"they":[374],"vary":[375],"across":[376],"lengths":[378],"sequences.":[381]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
