{"id":"https://openalex.org/W2117060467","doi":"https://doi.org/10.1093/bioinformatics/bti719","title":"ConFind: a robust tool for conserved sequence identification","display_name":"ConFind: a robust tool for conserved sequence identification","publication_year":2005,"publication_date":"2005-10-20","ids":{"openalex":"https://openalex.org/W2117060467","doi":"https://doi.org/10.1093/bioinformatics/bti719","mag":"2117060467","pmid":"https://pubmed.ncbi.nlm.nih.gov/16239306"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti719","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti719","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/24/4420/50566251/bioinformatics_21_24_4420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/24/4420/50566251/bioinformatics_21_24_4420.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048368902","display_name":"James A. Smagala","orcid":null},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"James A. Smagala","raw_affiliation_strings":["Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084877778","display_name":"Erica D. Dawson","orcid":"https://orcid.org/0000-0002-1743-2956"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erica D. Dawson","raw_affiliation_strings":["Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030096767","display_name":"Martin Mehlmann","orcid":null},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin Mehlmann","raw_affiliation_strings":["Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054166853","display_name":"Michael B. Townsend","orcid":"https://orcid.org/0000-0002-0354-7437"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael B. Townsend","raw_affiliation_strings":["Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056457744","display_name":"Robert D. Kuchta","orcid":"https://orcid.org/0000-0003-3179-0239"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert D. Kuchta","raw_affiliation_strings":["Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086118383","display_name":"Kathy L. Rowlen","orcid":null},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kathy L. Rowlen","raw_affiliation_strings":["Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, The University of Colorado at Boulder \u00a0 UCB #215, Boulder, CO 80309, USA","institution_ids":["https://openalex.org/I188538660"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5048368902"],"corresponding_institution_ids":["https://openalex.org/I188538660"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8615,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.71483777,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"21","issue":"24","first_page":"4420","last_page":"4422"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9879000186920166,"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":0.9879000186920166,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9305999875068665,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9265000224113464,"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/identification","display_name":"Identification (biology)","score":0.717928946018219},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6422315835952759},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6087148785591125},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5773659944534302},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.49030759930610657},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4508473873138428},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3388131856918335},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2988511621952057},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.24136939644813538},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1839277446269989},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09353789687156677},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.059984058141708374}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.717928946018219},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6422315835952759},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6087148785591125},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5773659944534302},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.49030759930610657},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4508473873138428},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3388131856918335},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2988511621952057},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.24136939644813538},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1839277446269989},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09353789687156677},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.059984058141708374}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004279","descriptor_name":"DNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009439","descriptor_name":"Neuraminidase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009439","descriptor_name":"Neuraminidase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009439","descriptor_name":"Neuraminidase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti719","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti719","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/24/4420/50566251/bioinformatics_21_24_4420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16239306","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16239306","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti719","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti719","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/24/4420/50566251/bioinformatics_21_24_4420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.7200000286102295,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2117060467.pdf","grobid_xml":"https://content.openalex.org/works/W2117060467.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1513910712","https://openalex.org/W1972624967","https://openalex.org/W2005965677","https://openalex.org/W2041001568","https://openalex.org/W2049105549","https://openalex.org/W2070951218","https://openalex.org/W2088366554","https://openalex.org/W2135272495"],"related_works":["https://openalex.org/W2181549235","https://openalex.org/W1973727281","https://openalex.org/W1996543580","https://openalex.org/W2046212479","https://openalex.org/W3209520725","https://openalex.org/W2003319012","https://openalex.org/W2031006065","https://openalex.org/W2044507120","https://openalex.org/W2514476306","https://openalex.org/W2023479323"],"abstract_inverted_index":{"ConFind":[0],"requires":[1],"Python":[2,5],"2.3,":[3],"but":[4],"2.4":[6],"or":[7],"an":[8],"upgrade":[9],"of":[10],"the":[11],"optparse":[12],"module":[13],"to":[14,23],"Optik":[15],"1.5":[16],"is":[17,21],"suggested.":[18],"The":[19],"program":[20],"known":[22],"run":[24],"under":[25],"Linux":[26],"and":[27],"DOS.":[28]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
