{"id":"https://openalex.org/W2113892097","doi":"https://doi.org/10.1186/1471-2105-6-279","title":"Computational identification of strain-, species- and genus-specific proteins","display_name":"Computational identification of strain-, species- and genus-specific proteins","publication_year":2005,"publication_date":"2005-11-23","ids":{"openalex":"https://openalex.org/W2113892097","doi":"https://doi.org/10.1186/1471-2105-6-279","mag":"2113892097","pmid":"https://pubmed.ncbi.nlm.nih.gov/16305751"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-6-279","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-279","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-279","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-279","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020517234","display_name":"Raja Mazumder","orcid":"https://orcid.org/0000-0001-8823-9945"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Raja Mazumder","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057-1414, USA. rm285@georgetown.edu","Department of Biochemistry & Molecular Biology, Georgetown University Medical Center, Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057-1414, USA. rm285@georgetown.edu","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, Georgetown University Medical Center, Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005555412","display_name":"Darren A. Natale","orcid":"https://orcid.org/0000-0001-5809-9523"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Darren A Natale","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Rd., NW, Washington, DC, 20057-1414, USA","Department of Biochemistry & Molecular Biology, Georgetown University Medical Center, Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Rd., NW, Washington, DC, 20057-1414, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, Georgetown University Medical Center, Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sudhir Murthy","orcid":null},"institutions":[{"id":"https://openalex.org/I1302767020","display_name":"District of Columbia Water and Sewer Authority","ror":"https://ror.org/029yh7e40","country_code":"US","type":"government","lineage":["https://openalex.org/I1302767020"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sudhir Murthy","raw_affiliation_strings":["DCWASA-DWT, 5000 Overlook Ave., SW, Washington, DC, 20032, USA","DCWASA-DWT, Washington, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DCWASA-DWT, 5000 Overlook Ave., SW, Washington, DC, 20032, USA","institution_ids":["https://openalex.org/I1302767020"]},{"raw_affiliation_string":"DCWASA-DWT, Washington, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064293072","display_name":"Rathi D. Thiagarajan","orcid":null},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rathi Thiagarajan","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Rd., NW, Washington, DC, 20057-1414, USA","Department of Biochemistry & Molecular Biology, Georgetown University Medical Center, Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Rd., NW, Washington, DC, 20057-1414, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, Georgetown University Medical Center, Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053761444","display_name":"Cathy Wu","orcid":"https://orcid.org/0000-0001-6379-8601"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cathy H Wu","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Rd., NW, Washington, DC, 20057-1414, USA","Department of Biochemistry & Molecular Biology, Georgetown University Medical Center, Washington, DC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Rd., NW, Washington, DC, 20057-1414, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology, Georgetown University Medical Center, Washington, DC, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5020517234"],"corresponding_institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6279,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.66908094,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"6","issue":"1","first_page":"279","last_page":"279"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.21889999508857727,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.21889999508857727,"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":0.17910000681877136,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.05530000105500221,"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/proteome","display_name":"Proteome","score":0.6478800177574158},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.56742262840271},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5596792697906494},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5429487228393555},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.4975791275501251},{"id":"https://openalex.org/keywords/genus","display_name":"Genus","score":0.4924999177455902},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.46713972091674805},{"id":"https://openalex.org/keywords/strain","display_name":"Strain (injury)","score":0.4505314826965332},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.4100199341773987},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.379226416349411},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32017457485198975},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2563961148262024},{"id":"https://openalex.org/keywords/zoology","display_name":"Zoology","score":0.0877058207988739},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.07051530480384827}],"concepts":[{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6478800177574158},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.56742262840271},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5596792697906494},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5429487228393555},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.4975791275501251},{"id":"https://openalex.org/C157369684","wikidata":"https://www.wikidata.org/wiki/Q34740","display_name":"Genus","level":2,"score":0.4924999177455902},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.46713972091674805},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.4505314826965332},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.4100199341773987},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.379226416349411},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32017457485198975},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2563961148262024},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.0877058207988739},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.07051530480384827},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"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":"D001408","descriptor_name":"Bacillus anthracis","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001408","descriptor_name":"Bacillus anthracis","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001408","descriptor_name":"Bacillus anthracis","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002965","descriptor_name":"Classification","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-6-279","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-279","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-279","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16305751","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16305751","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:238f8aa390bf422ea93860ff1feea9ee","is_oa":true,"landing_page_url":"https://doaj.org/article/238f8aa390bf422ea93860ff1feea9ee","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,"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":"BMC Bioinformatics, Vol 6, Iss 1, p 279 (2005)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1310627","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1310627","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-6-279","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-6-279","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-6-279","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3518280821","display_name":null,"funder_award_id":"U01-HG02712","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4806228030","display_name":null,"funder_award_id":"U01 HG002712","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320309122","display_name":"District of Columbia Water and Sewer Authority","ror":"https://ror.org/029yh7e40"},{"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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2113892097.pdf","grobid_xml":"https://content.openalex.org/works/W2113892097.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W160224279","https://openalex.org/W1588180012","https://openalex.org/W1971147414","https://openalex.org/W1990453950","https://openalex.org/W2008080212","https://openalex.org/W2024011853","https://openalex.org/W2029372233","https://openalex.org/W2079213755","https://openalex.org/W2099836442","https://openalex.org/W2112856567","https://openalex.org/W2128549389","https://openalex.org/W2128897400","https://openalex.org/W2131924932","https://openalex.org/W2134153749","https://openalex.org/W2142887093","https://openalex.org/W2144362290","https://openalex.org/W2148381092","https://openalex.org/W2148474327","https://openalex.org/W2151831732","https://openalex.org/W2158714788","https://openalex.org/W2160072419","https://openalex.org/W2161062388","https://openalex.org/W2162888916","https://openalex.org/W2169748335"],"related_works":["https://openalex.org/W4223896405","https://openalex.org/W2059629050","https://openalex.org/W2074740504","https://openalex.org/W3013644380","https://openalex.org/W1996935079","https://openalex.org/W3210243923","https://openalex.org/W2145833061","https://openalex.org/W2258998699","https://openalex.org/W1998405066","https://openalex.org/W2171737904"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,205,265],"identification":[2],"of":[3,52,57,192,199,228,245,248,256,297],"unique":[4,93,203,237,249],"proteins":[5,20,38,68,126,229,250,298],"at":[6,238,290],"different":[7],"taxonomic":[8],"levels":[9],"has":[10],"both":[11],"scientific":[12],"and":[13,18,31,54,66,69,124,195,214,241,274,281,307],"practical":[14],"value.":[15],"Strain-,":[16],"species-":[17,123],"genus-specific":[19,67,125],"can":[21,39,271],"provide":[22],"insight":[23],"into":[24],"the":[25,72,115,132,136,143,154,160,166,175,185,190,197,200,220,239,246,278,309],"criteria":[26],"that":[27,219,232,252],"define":[28],"an":[29,105],"organism":[30],"its":[32],"relationship":[33],"with":[34,230],"close":[35],"relatives.":[36],"Such":[37],"also":[40],"serve":[41],"as":[42,135],"taxon-specific":[43],"diagnostic":[44],"targets.":[45],"DESCRIPTION:":[46],"A":[47],"pipeline":[48],"using":[49,96,131,174,184],"a":[50,80,85,97,295,301,305],"combination":[51],"computational":[53],"manual":[55],"analyses":[56],"BLAST":[58,162,222],"results":[59],"was":[60,208],"developed":[61],"to":[62,70,91,102,171,210,300],"identify":[63],"strain-,":[64,122],"species-,":[65],"catalog":[71],"closest":[73],"sequenced":[74],"relative":[75],"for":[76,151,202],"each":[77],"protein":[78,99,111],"in":[79,159,263],"proteome.":[81],"Proteins":[82],"encoded":[83,113],"by":[84,114],"given":[86],"strain":[87],"are":[88,148,182,254],"preliminarily":[89],"considered":[90,236],"be":[92,235,261,272],"if":[94,129,153],"BLAST,":[95,130],"comprehensive":[98],"database,":[100],"fails":[101],"retrieve":[103,142,172],"(with":[104],"e-value":[106],"better":[107],"than":[108],"0.001)":[109],"any":[110],"not":[112,141,165],"query":[116,137,145,156],"strain,":[117,306],"species":[118,242,303],"or":[119,128,259,304],"genus":[120,240],"(for":[121],"respectively),":[127],"best":[133,167],"hit":[134],"(reverse":[138],"BLAST),":[139],"does":[140],"initial":[144,155],"protein.":[146],"Results":[147],"manually":[149],"inspected":[150],"homology":[152],"is":[157,164],"retrieved":[158,193],"reverse":[161,221],"but":[163],"hit.":[168],"Sequences":[169],"unlikely":[170],"homologs":[173,194,231],"default":[176],"BLOSUM62":[177],"matrix":[178],"(usually":[179],"short":[180],"sequences)":[181],"re-tested":[183],"PAM30":[186],"matrix,":[187],"thereby":[188],"increasing":[189,196],"number":[191],"stringency":[198],"search":[201],"proteins.":[204],"above":[206],"protocol":[207],"used":[209],"examine":[211],"several":[212],"food-":[213],"water-borne":[215],"pathogens.":[216],"We":[217],"find":[218],"step":[223],"filters":[224],"out":[225],"about":[226],"22%":[227],"would":[233],"otherwise":[234],"levels.":[243],"Analysis":[244],"annotations":[247],"reveals":[251],"many":[253],"remnants":[255],"prophage":[257],"proteins,":[258],"may":[260],"involved":[262],"virulence.":[264],"data":[266],"generated":[267],"from":[268,277],"this":[269],"study":[270],"accessed":[273],"further":[275],"evaluated":[276],"CUPID":[279,293],"(Core":[280],"Unique":[282],"Protein":[283],"Identification)":[284],"system":[285],"web":[286],"site":[287],"(updated":[288],"semi-annually)":[289],"http://pir.georgetown.edu/cupid.":[291],"CONCLUSION:":[292],"provides":[294],"set":[296],"specific":[299],"genus,":[302],"identifies":[308],"most":[310],"closely":[311],"related":[312],"organism.":[313]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}