{"id":"https://openalex.org/W80997463","doi":"https://doi.org/10.2144/00286bc01","title":"Strategies for Searching Sequence Databases","display_name":"Strategies for Searching Sequence Databases","publication_year":2000,"publication_date":"2000-06-01","ids":{"openalex":"https://openalex.org/W80997463","doi":"https://doi.org/10.2144/00286bc01","mag":"80997463","pmid":"https://pubmed.ncbi.nlm.nih.gov/10868283"},"language":"en","primary_location":{"id":"doi:10.2144/00286bc01","doi":"https://doi.org/10.2144/00286bc01","is_oa":true,"landing_page_url":"https://doi.org/10.2144/00286bc01","pdf_url":"https://www.future-science.com/doi/pdf/10.2144/00286bc01","source":{"id":"https://openalex.org/S79990748","display_name":"BioTechniques","issn_l":"0736-6205","issn":["0736-6205","1940-9818"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320316","host_organization_name":"Future Science Ltd","host_organization_lineage":["https://openalex.org/P4310320316"],"host_organization_lineage_names":["Future Science Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioTechniques","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.future-science.com/doi/pdf/10.2144/00286bc01","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020668549","display_name":"Hugh B. Nicholas","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I35765314","display_name":"Pittsburgh Supercomputing Center","ror":"https://ror.org/04tac1482","country_code":"US","type":"facility","lineage":["https://openalex.org/I35765314"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hugh B. Nicholas","raw_affiliation_strings":["Pittsburgh Supercomputing Center, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pittsburgh Supercomputing Center, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I35765314"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042698432","display_name":"David W. Deerfield","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I35765314","display_name":"Pittsburgh Supercomputing Center","ror":"https://ror.org/04tac1482","country_code":"US","type":"facility","lineage":["https://openalex.org/I35765314"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David W. Deerfield","raw_affiliation_strings":["Pittsburgh Supercomputing Center, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pittsburgh Supercomputing Center, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I35765314"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091840898","display_name":"Alexander J. Ropelewski","orcid":"https://orcid.org/0000-0001-6874-4477","observed_orcids":["https://orcid.org/0000-0001-6874-4477"]},"institutions":[{"id":"https://openalex.org/I35765314","display_name":"Pittsburgh Supercomputing Center","ror":"https://ror.org/04tac1482","country_code":"US","type":"facility","lineage":["https://openalex.org/I35765314"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander J. Ropelewski","raw_affiliation_strings":["Pittsburgh Supercomputing Center, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pittsburgh Supercomputing Center, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I35765314"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I35765314"],"apc_list":{"value":1415,"currency":"USD","value_usd":1415},"apc_paid":{"value":1415,"currency":"USD","value_usd":1415},"fwci":0.6758,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.65295928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":94},"biblio":{"volume":"28","issue":"6","first_page":"1174","last_page":"1191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9648000001907349,"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":0.9648000001907349,"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":0.018699999898672104,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.008100000210106373,"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/sequence-database-searching","display_name":"sequence database searching","score":0.8389999866485596},{"id":"https://openalex.org/keywords/sequence-alignment-algorithms","display_name":"sequence alignment algorithms","score":0.6819999814033508},{"id":"https://openalex.org/keywords/substitution-matrices","display_name":"substitution matrices","score":0.9850000143051147},{"id":"https://openalex.org/keywords/gap-model","display_name":"gap model","score":0.8949999809265137},{"id":"https://openalex.org/keywords/sequence-evolution-models","display_name":"sequence evolution models","score":0.8859999775886536},{"id":"https://openalex.org/keywords/evolutionary-distance","display_name":"phylogenetic distance","score":0.5090000033378601},{"id":"https://openalex.org/keywords/blast","display_name":"BLAST","score":0.7080000042915344},{"id":"https://openalex.org/keywords/fasta","display_name":"FASTA","score":0.6859999895095825}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7360249757766724},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6033773422241211},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.5730408430099487},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.5365749597549438},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.4270819127559662},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.41807496547698975},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3992149829864502},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3555469512939453},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.119487464427948},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0915212631225586},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06377282738685608},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","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}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.2144/00286bc01","doi":"https://doi.org/10.2144/00286bc01","is_oa":true,"landing_page_url":"https://doi.org/10.2144/00286bc01","pdf_url":"https://www.future-science.com/doi/pdf/10.2144/00286bc01","source":{"id":"https://openalex.org/S79990748","display_name":"BioTechniques","issn_l":"0736-6205","issn":["0736-6205","1940-9818"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320316","host_organization_name":"Future Science Ltd","host_organization_lineage":["https://openalex.org/P4310320316"],"host_organization_lineage_names":["Future Science Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioTechniques","raw_type":"journal-article"},{"id":"pmid:10868283","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/10868283","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,"listed_in":[],"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":"BioTechniques","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:4cc47a63e4544b9ab5d50984c1c5143a","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/4cc47a63e4544b9ab5d50984c1c5143a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioTechniques, Vol 28, Iss 6, Pp 1174-1191 (2000)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.2144/00286bc01","doi":"https://doi.org/10.2144/00286bc01","is_oa":true,"landing_page_url":"https://doi.org/10.2144/00286bc01","pdf_url":"https://www.future-science.com/doi/pdf/10.2144/00286bc01","source":{"id":"https://openalex.org/S79990748","display_name":"BioTechniques","issn_l":"0736-6205","issn":["0736-6205","1940-9818"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320316","host_organization_name":"Future Science Ltd","host_organization_lineage":["https://openalex.org/P4310320316"],"host_organization_lineage_names":["Future Science Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioTechniques","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality education","score":0.41999998688697815}],"study_designs":[],"awards":[{"id":"https://openalex.org/G2805697681","display_name":null,"funder_award_id":"T15 HG00015","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G3339726651","display_name":null,"funder_award_id":"P41RR06009","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G9000063808","display_name":null,"funder_award_id":"P41RR06009","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000155257","display_name":null,"funder_award_id":"RR06009","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320308668","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60"},{"id":"https://openalex.org/F4320309650","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W80997463.pdf","grobid_xml":"https://content.openalex.org/works/W80997463.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W649798380","https://openalex.org/W1500214331","https://openalex.org/W1965998064","https://openalex.org/W1973578915","https://openalex.org/W1977618577","https://openalex.org/W1983698816","https://openalex.org/W1992344680","https://openalex.org/W2002180966","https://openalex.org/W2014660704","https://openalex.org/W2014840152","https://openalex.org/W2015292449","https://openalex.org/W2022057459","https://openalex.org/W2025313270","https://openalex.org/W2026257220","https://openalex.org/W2055043387","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2089499735","https://openalex.org/W2092979861","https://openalex.org/W2094519647","https://openalex.org/W2108215151","https://openalex.org/W2113398700","https://openalex.org/W2143210482","https://openalex.org/W2158714788","https://openalex.org/W2600349519"],"related_works":["https://openalex.org/W3208095355","https://openalex.org/W2052507016","https://openalex.org/W2180461068","https://openalex.org/W2177370417","https://openalex.org/W2051816080","https://openalex.org/W2156730189","https://openalex.org/W2362702465","https://openalex.org/W2041132749","https://openalex.org/W2136066520","https://openalex.org/W2354598492"],"abstract_inverted_index":{"We":[0,74],"provide":[1],"a":[2,11,77],"detailed":[3],"overview":[4],"of":[5,18,26,41,47,71,79],"the":[6,16,38,44,50,54,67,72],"choices":[7,28],"inherent":[8],"in":[9],"performing":[10,83],"sequence":[12,42,52],"database":[13,55],"search,":[14],"including":[15],"choice":[17],"algorithm,":[19],"substitution":[20],"matrix":[21],"and":[22,53,69,90],"gap":[23],"model.":[24],"Each":[25],"these":[27,84],"has":[29],"implications":[30],"that":[31],"can":[32],"be":[33],"described":[34],"as":[35,64,66],"restrictions":[36],"on":[37,87],"underlying":[39],"model":[40],"evolution,":[43],"expected":[45],"degree":[46],"divergence":[48],"between":[49],"query":[51],"sequences":[56],"(if":[57],"one":[58],"uses":[59],"an":[60],"evolutionary":[61],"based":[62,86],"matrix),":[63],"well":[65],"sensitivity":[68],"selectivity":[70],"search.":[73],"conclude":[75],"with":[76],"series":[78],"recommendations":[80],"for":[81],"researchers":[82],"searches":[85],"our":[88],"experience":[89],"literature":[91],"studies.":[92]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2025-10-10T00:00:00"}