{"id":"https://openalex.org/W2546852653","doi":"https://doi.org/10.1109/tcyb.2016.2621129","title":"A Characteristic-Based Framework for Multiple Sequence Aligners","display_name":"A Characteristic-Based Framework for Multiple Sequence Aligners","publication_year":2016,"publication_date":"2016-11-02","ids":{"openalex":"https://openalex.org/W2546852653","doi":"https://doi.org/10.1109/tcyb.2016.2621129","mag":"2546852653","pmid":"https://pubmed.ncbi.nlm.nih.gov/27831898"},"language":"en","primary_location":{"id":"doi:10.1109/tcyb.2016.2621129","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcyb.2016.2621129","pdf_url":null,"source":{"id":"https://openalex.org/S4210191041","display_name":"IEEE Transactions on Cybernetics","issn_l":"2168-2267","issn":["2168-2267","2168-2275"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Cybernetics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/10362/146530","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009435283","display_name":"\u00c1lvaro Rubio\u2010Largo","orcid":"https://orcid.org/0000-0003-2999-4304"},"institutions":[{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Alvaro Rubio-Largo","raw_affiliation_strings":["NOVA Information Management School, Universidade Nova de Lisboa, Lisbon, Portugal"],"raw_orcid":"https://orcid.org/0000-0003-2999-4304","affiliations":[{"raw_affiliation_string":"NOVA Information Management School, Universidade Nova de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I83558840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056916227","display_name":"Leonardo Vanneschi","orcid":"https://orcid.org/0000-0003-4732-3328"},"institutions":[{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Leonardo Vanneschi","raw_affiliation_strings":["NOVA Information Management School, Universidade Nova de Lisboa, Lisbon, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NOVA Information Management School, Universidade Nova de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I83558840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087976149","display_name":"Mauro Castelli","orcid":"https://orcid.org/0000-0002-8793-1451"},"institutions":[{"id":"https://openalex.org/I83558840","display_name":"Universidade Nova de Lisboa","ror":"https://ror.org/02xankh89","country_code":"PT","type":"education","lineage":["https://openalex.org/I83558840"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Mauro Castelli","raw_affiliation_strings":["NOVA Information Management School, Universidade Nova de Lisboa, Lisbon, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NOVA Information Management School, Universidade Nova de Lisboa, Lisbon, Portugal","institution_ids":["https://openalex.org/I83558840"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049408851","display_name":"Miguel \u00c1. Vega-Rodr\u00edguez","orcid":"https://orcid.org/0000-0002-3003-758X"},"institutions":[{"id":"https://openalex.org/I80606768","display_name":"Universidad de Extremadura","ror":"https://ror.org/0174shg90","country_code":"ES","type":"education","lineage":["https://openalex.org/I80606768"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miguel A. Vega-Rodriguez","raw_affiliation_strings":["Department of Computer and Communications Technologies, University of Extremadura, Caceres, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Communications Technologies, University of Extremadura, Caceres, Spain","institution_ids":["https://openalex.org/I80606768"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.3669,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.82229826,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"48","issue":"1","first_page":"41","last_page":"51"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9878000020980835,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9800000190734863,"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/benchmark","display_name":"Benchmark (surveying)","score":0.8541427850723267},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.7136175632476807},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.70728999376297},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6827903985977173},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6773403882980347},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6438398361206055},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.6427669525146484},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5994704961776733},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5294579863548279},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43087005615234375},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3629099130630493},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35098230838775635},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.300618439912796},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.12871044874191284},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12783601880073547},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07916605472564697}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.8541427850723267},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.7136175632476807},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.70728999376297},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6827903985977173},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6773403882980347},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6438398361206055},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.6427669525146484},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5994704961776733},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5294579863548279},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43087005615234375},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3629099130630493},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35098230838775635},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.300618439912796},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.12871044874191284},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12783601880073547},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07916605472564697},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/tcyb.2016.2621129","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcyb.2016.2621129","pdf_url":null,"source":{"id":"https://openalex.org/S4210191041","display_name":"IEEE Transactions on Cybernetics","issn_l":"2168-2267","issn":["2168-2267","2168-2275"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Cybernetics","raw_type":"journal-article"},{"id":"pmid:27831898","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27831898","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on cybernetics","raw_type":null},{"id":"pmh:oai:run.unl.pt:10362/146530","is_oa":true,"landing_page_url":"http://hdl.handle.net/10362/146530","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"}],"best_oa_location":{"id":"pmh:oai:run.unl.pt:10362/146530","is_oa":true,"landing_page_url":"http://hdl.handle.net/10362/146530","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6600000262260437,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1202009969","display_name":null,"funder_award_id":"TIN2016-76259-P","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G3980006358","display_name":null,"funder_award_id":"TIN2016-76259-P","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G7423104835","display_name":null,"funder_award_id":"SFRH/BPD/100872/2014","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W290667870","https://openalex.org/W1646393397","https://openalex.org/W1969153299","https://openalex.org/W1979081881","https://openalex.org/W1996681309","https://openalex.org/W2005313213","https://openalex.org/W2005336557","https://openalex.org/W2011289056","https://openalex.org/W2014747921","https://openalex.org/W2059655077","https://openalex.org/W2077215180","https://openalex.org/W2087528369","https://openalex.org/W2106882534","https://openalex.org/W2120866529","https://openalex.org/W2121691652","https://openalex.org/W2127774996","https://openalex.org/W2128613007","https://openalex.org/W2130479394","https://openalex.org/W2132926880","https://openalex.org/W2136570298","https://openalex.org/W2140872496","https://openalex.org/W2141119792","https://openalex.org/W2143292980","https://openalex.org/W2143357251","https://openalex.org/W2144362290","https://openalex.org/W2152195021","https://openalex.org/W2158714788","https://openalex.org/W2166718648","https://openalex.org/W2170831688","https://openalex.org/W2187537484","https://openalex.org/W2950680102","https://openalex.org/W4247510436"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2029514038","https://openalex.org/W2141411672","https://openalex.org/W2133116680","https://openalex.org/W1482324242","https://openalex.org/W2468116983","https://openalex.org/W2088487249","https://openalex.org/W187239587","https://openalex.org/W2158700816"],"abstract_inverted_index":{"The":[0,115,188,217],"multiple":[1,112,161,221],"sequence":[2,39,113,162,184,222],"alignment":[3,13,40,79,180,185,193],"is":[4,72,224],"a":[5,27,57,108,212],"well-known":[6,160],"bioinformatics":[7],"problem":[8],"that":[9,191],"consists":[10],"in":[11,208],"the":[12,25,63,69,75,78,82,96,100,118,133,136,154,159,192,204],"of":[14,29,81,99,117,125,144,197,215],"three":[15],"or":[16,21,48],"more":[17],"biological":[18,38,97],"sequences":[19,65,146],"(protein":[20],"nucleic":[22],"acid).":[23],"In":[24,103,150],"literature,":[26],"number":[28],"tools":[30],"have":[31,157],"been":[32],"proposed":[33,205],"for":[34,61,111,141,220,227],"dealing":[35],"with":[36,135,147,169,203,211],"this":[37,104],"problem,":[41],"such":[42,172],"as":[43,173],"progressive":[44],"methods,":[45,47],"consistency-based":[46],"iterative":[49],"methods;":[50],"among":[51],"others.":[52],"These":[53],"aligners":[54,223],"often":[55],"use":[56],"default":[58,70],"parameter":[59,90,138],"configuration":[60,71,139],"all":[62],"input":[64,101,123],"to":[66,152],"align.":[67],"However,":[68],"not":[73],"always":[74],"best":[76,137],"choice,":[77],"accuracy":[80,194],"tool":[83],"may":[84],"be":[85,200],"highly":[86],"boosted":[87],"if":[88],"specific":[89],"configurations":[91],"are":[92],"used,":[93],"depending":[94],"on":[95],"characteristics":[98,130],"sequences.":[102],"paper,":[105],"we":[106,156],"propose":[107],"characteristic-based":[109,218],"framework":[110,119,219],"aligners.":[114],"idea":[116],"is,":[120],"given":[121],"an":[122],"set":[124,143],"unaligned":[126,145],"sequences,":[127],"extract":[128],"its":[129],"and":[131,183,195],"run":[132],"aligner":[134,168],"found":[140],"another":[142],"similar":[148],"characteristics.":[149],"order":[151],"test":[153],"framework,":[155,206],"used":[158],"comparison":[163],"by":[164],"log-expectation":[165],"(MUSCLE)":[166],"v3.8":[167],"different":[170],"benchmarks,":[171],"benchmark":[174,181,186],"alignments":[175],"database":[176],"v3.0,":[177],"protein":[178],"reference":[179],"v4.0,":[182],"v1.65.":[187],"results":[189],"shown":[190],"conservation":[196],"MUSCLE":[198],"might":[199],"greatly":[201],"improved":[202],"specially":[207],"those":[209],"scenarios":[210],"low":[213],"percentage":[214],"identity.":[216],"freely":[225],"available":[226],"downloading":[228],"at":[229],"http://arco.unex.es/arl/fwk-msa/cbf-msa.zip.":[230]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
