{"id":"https://openalex.org/W1508164074","doi":"https://doi.org/10.23919/ecc.2003.7086563","title":"Alignment algorithms revisited: Alignment algorithms for low similarity protein sequence comparisons","display_name":"Alignment algorithms revisited: Alignment algorithms for low similarity protein sequence comparisons","publication_year":2003,"publication_date":"2003-09-01","ids":{"openalex":"https://openalex.org/W1508164074","doi":"https://doi.org/10.23919/ecc.2003.7086563","mag":"1508164074"},"language":"en","primary_location":{"id":"doi:10.23919/ecc.2003.7086563","is_oa":false,"landing_page_url":"https://doi.org/10.23919/ecc.2003.7086563","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2003 European Control Conference (ECC)","raw_type":"proceedings-article"},"type":"article","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/A5077067779","display_name":"Michael J. Wise","orcid":"https://orcid.org/0000-0001-6559-4303"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Michael J. Wise","raw_affiliation_strings":["Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5077067779"],"corresponding_institution_ids":["https://openalex.org/I241749"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.04536535,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"3386","last_page":"3391"},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9966999888420105,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9865000247955322,"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/smith\u2013waterman-algorithm","display_name":"Smith\u2013Waterman algorithm","score":0.8997451066970825},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.7943572402000427},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6579293608665466},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6330562829971313},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.5451461672782898},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5213078856468201},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5096118450164795},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4716167747974396},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4146064817905426},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2715209722518921},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.08005961775779724}],"concepts":[{"id":"https://openalex.org/C72802188","wikidata":"https://www.wikidata.org/wiki/Q1683352","display_name":"Smith\u2013Waterman algorithm","level":5,"score":0.8997451066970825},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.7943572402000427},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6579293608665466},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6330562829971313},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.5451461672782898},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5213078856468201},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5096118450164795},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4716167747974396},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4146064817905426},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2715209722518921},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.08005961775779724},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.23919/ecc.2003.7086563","is_oa":false,"landing_page_url":"https://doi.org/10.23919/ecc.2003.7086563","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2003 European Control Conference (ECC)","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.586.3289","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.586.3289","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.pam1.bcs.uwa.edu.au/~michaelw/ftp/doc/align_full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320307115","display_name":"Bristol-Myers Squibb","ror":"https://ror.org/00gtmwv55"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1491040459","https://openalex.org/W1491063910","https://openalex.org/W1502621331","https://openalex.org/W1526009719","https://openalex.org/W1529209937","https://openalex.org/W1659313070","https://openalex.org/W1670263352","https://openalex.org/W1783219955","https://openalex.org/W2022057459","https://openalex.org/W2036792999","https://openalex.org/W2055043387","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2089499735","https://openalex.org/W2099254366","https://openalex.org/W2108067237","https://openalex.org/W2117077088","https://openalex.org/W2137995988","https://openalex.org/W2157975034","https://openalex.org/W2683236244","https://openalex.org/W2752885492","https://openalex.org/W4210727445"],"related_works":["https://openalex.org/W2056158083","https://openalex.org/W2130740364","https://openalex.org/W88386512","https://openalex.org/W3210186669","https://openalex.org/W3183986862","https://openalex.org/W1972247471","https://openalex.org/W1967637578","https://openalex.org/W3000366369","https://openalex.org/W2351540725","https://openalex.org/W2350395044"],"abstract_inverted_index":{"The":[0],"Smith-Waterman":[1,84],"local":[2,75,122,136,146],"alignment":[3,78],"algorithm":[4,39,85],"is":[5,16,30,86],"the":[6,35,72,83,102,107],"method":[7],"of":[8,37,74,133],"choice":[9],"for":[10,23,42],"protein":[11,26],"database":[12],"searches":[13],"because":[14],"it":[15,29],"often":[17,62],"able":[18],"to":[19,47,88,101,135,145,148],"detect":[20],"remote":[21],"homologues":[22],"a":[24,48,96,129],"query":[25,50],"sequence.":[27],"However,":[28,110],"also":[31],"well":[32],"known":[33],"that":[34],"reliability":[36],"this":[38],"degrades":[40],"sharply":[41],"proteins":[43,94],"with":[44],"low":[45],"similarity":[46],"given":[49],"\u2014":[51],"so-called":[52],"\"twilight":[53],"zone\"":[54],"matches.":[55],"In":[56,124],"these":[57],"situations,":[58],"global":[59,77,116,126],"alignments":[60],"are":[61,118,157],"employed,":[63],"based":[64],"largely":[65],"on":[66],"anecdotal":[67],"evidence.":[68],"This":[69],"study":[70],"re-examines":[71],"efficacy":[73],"versus":[76],"algorithms.":[79],"Among":[80],"other":[81],"results,":[82],"found":[87],"be":[89,141],"most":[90],"effective":[91,120],"when":[92,111,153],"two":[93],"have":[95,106],"common":[97],"domain":[98],"(i.e.":[99],"belong":[100],"same":[103,108],"subgroup)":[104],"or":[105],"function.":[109],"only":[112],"weak":[113],"relationships":[114],"exist,":[115],"methods":[117,127,137,147],"more":[119],"than":[121],"ones.":[123],"addition,":[125],"provide":[128],"somewhat":[130],"different":[131],"point":[132],"view":[134],"and":[138],"can":[139],"therefore":[140],"used":[142],"in":[143],"addition":[144],"improve":[149],"search":[150],"accuracy,":[151],"even":[152],"higher":[154],"level":[155],"matches":[156],"possible.":[158]},"counts_by_year":[{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
