{"id":"https://openalex.org/W1995229312","doi":"https://doi.org/10.1142/s0219720005001247","title":"SPIDER: SOFTWARE FOR PROTEIN IDENTIFICATION FROM SEQUENCE TAGS WITH <i>DE NOVO</i> SEQUENCING ERROR","display_name":"SPIDER: SOFTWARE FOR PROTEIN IDENTIFICATION FROM SEQUENCE TAGS WITH <i>DE NOVO</i> SEQUENCING ERROR","publication_year":2005,"publication_date":"2005-06-01","ids":{"openalex":"https://openalex.org/W1995229312","doi":"https://doi.org/10.1142/s0219720005001247","mag":"1995229312","pmid":"https://pubmed.ncbi.nlm.nih.gov/16108090"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720005001247","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720005001247","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5053254893","display_name":"Yonghua Han","orcid":"https://orcid.org/0000-0001-9305-2536"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"YONGHUA HAN","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada","Department of Computer Science, University of Western Ontario, London, Ontario, CANADA N6A 5B7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, CANADA N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100749727","display_name":"Bin Ma","orcid":"https://orcid.org/0000-0001-6254-4087"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"BIN MA","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada","Department of Computer Science, University of Western Ontario, London, Ontario, CANADA N6A 5B7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, CANADA N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081729547","display_name":"Kaizhong Zhang","orcid":"https://orcid.org/0000-0003-1734-5921"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"KAIZHONG ZHANG","raw_affiliation_strings":["Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada","Department of Computer Science, University of Western Ontario, London, Ontario, CANADA N6A 5B7, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Computer Science, University of Western Ontario, London, Ontario, CANADA N6A 5B7, Canada","institution_ids":["https://openalex.org/I125749732"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":null,"apc_paid":null,"fwci":5.9326,"has_fulltext":false,"cited_by_count":219,"citation_normalized_percentile":{"value":0.96773978,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"03","issue":"03","first_page":"697","last_page":"716"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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/software","display_name":"Software","score":0.6255618333816528},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5722715854644775},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5368108749389648},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5126494765281677},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48434507846832275},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.4833543002605438},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.4787815809249878},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.45570334792137146},{"id":"https://openalex.org/keywords/protein-methods","display_name":"Protein methods","score":0.44004952907562256},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4374794065952301},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.43310460448265076},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2780400216579437},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14844748377799988},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.135732501745224},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.071637362241745}],"concepts":[{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6255618333816528},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5722715854644775},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5368108749389648},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5126494765281677},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48434507846832275},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.4833543002605438},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.4787815809249878},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.45570334792137146},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.44004952907562256},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4374794065952301},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.43310460448265076},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2780400216579437},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14844748377799988},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.135732501745224},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.071637362241745},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720005001247","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720005001247","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:16108090","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16108090","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.49000000953674316}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1970172743","https://openalex.org/W1971887998","https://openalex.org/W1981593008","https://openalex.org/W1987325064","https://openalex.org/W1995693931","https://openalex.org/W1996310600","https://openalex.org/W1999359367","https://openalex.org/W2001848433","https://openalex.org/W2003111732","https://openalex.org/W2008317045","https://openalex.org/W2015292449","https://openalex.org/W2023096047","https://openalex.org/W2026465178","https://openalex.org/W2034645824","https://openalex.org/W2035167912","https://openalex.org/W2035283832","https://openalex.org/W2038396508","https://openalex.org/W2055043387","https://openalex.org/W2058135122","https://openalex.org/W2059572899","https://openalex.org/W2083911564","https://openalex.org/W2120537063","https://openalex.org/W2127963907","https://openalex.org/W2128591967","https://openalex.org/W2143210482","https://openalex.org/W2158714788","https://openalex.org/W3136323740"],"related_works":["https://openalex.org/W3215016332","https://openalex.org/W2985880923","https://openalex.org/W2053028024","https://openalex.org/W1491924329","https://openalex.org/W2024383575","https://openalex.org/W2395301313","https://openalex.org/W1965617697","https://openalex.org/W2033162017","https://openalex.org/W2012033675","https://openalex.org/W2011602722"],"abstract_inverted_index":{"For":[0],"the":[1,38,45,52,55,71,102,121,146,151],"identification":[2],"of":[3,54,92,123,150],"novel":[4],"proteins":[5,56],"using":[6],"MS/MS,":[7],"de":[8,46,74],"novo":[9,47,75],"sequencing":[10,48,76],"software":[11,64,129],"computes":[12],"one":[13],"or":[14],"several":[15],"possible":[16],"amino":[17,35,93],"acid":[18,36],"sequences":[19,39,119],"(called":[20],"sequence":[21,113],"tags)":[22],"for":[23,70,120,139],"each":[24],"MS/MS":[25],"spectrum.":[26],"Those":[27],"tags":[28,114],"are":[29],"then":[30],"used":[31],"to":[32,111,117],"match,":[33],"accounting":[34],"mutations,":[37],"in":[40],"a":[41,90,107],"protein":[42,124],"database.":[43],"If":[44],"gives":[49,79],"correct":[50,82],"tags,":[51],"homologs":[53],"can":[57],"be":[58],"identified":[59],"by":[60,97],"this":[61],"approach":[62],"and":[63,125,134,148],"such":[65],"as":[66],"MS-BLAST":[67],"is":[68,88,95],"available":[69,136],"matching.":[72],"However,":[73],"very":[77],"often":[78],"only":[80],"partially":[81],"tags.":[83],"The":[84],"most":[85],"common":[86],"error":[87],"that":[89],"segment":[91,99],"acids":[94],"replaced":[96],"another":[98],"with":[100,115],"approximately":[101],"same":[103],"masses.":[104],"We":[105],"developed":[106,133],"new":[108],"efficient":[109],"algorithm":[110],"match":[112],"errors":[116],"database":[118],"purpose":[122],"peptide":[126],"identification.":[127],"A":[128],"package,":[130],"SPIDER,":[131],"was":[132],"made":[135],"on":[137],"Internet":[138],"free":[140],"public":[141],"use.":[142],"This":[143],"paper":[144],"describes":[145],"algorithms":[147],"features":[149],"SPIDER":[152],"software.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":15},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":15}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2016-06-24T00:00:00"}
