{"id":"https://openalex.org/W3193334963","doi":"https://doi.org/10.1093/bioinformatics/btab607","title":"GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data","display_name":"GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data","publication_year":2021,"publication_date":"2021-08-19","ids":{"openalex":"https://openalex.org/W3193334963","doi":"https://doi.org/10.1093/bioinformatics/btab607","mag":"3193334963","pmid":"https://pubmed.ncbi.nlm.nih.gov/34415321"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab607","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab607","pdf_url":null,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020756463","display_name":"Richard A. Stanton","orcid":"https://orcid.org/0000-0003-4810-7002"},"institutions":[{"id":"https://openalex.org/I1289490764","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12","country_code":"US","type":"government","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richard A Stanton","raw_affiliation_strings":["Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention , Atlanta, GA 30329, USA"],"raw_orcid":"https://orcid.org/0000-0003-4810-7002","affiliations":[{"raw_affiliation_string":"Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention , Atlanta, GA 30329, USA","institution_ids":["https://openalex.org/I1289490764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046936771","display_name":"Nicholas Vlachos","orcid":null},"institutions":[{"id":"https://openalex.org/I1289490764","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12","country_code":"US","type":"government","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Vlachos","raw_affiliation_strings":["Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention , Atlanta, GA 30329, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention , Atlanta, GA 30329, USA","institution_ids":["https://openalex.org/I1289490764"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002202077","display_name":"Alison Laufer Halpin","orcid":"https://orcid.org/0000-0003-1643-1617"},"institutions":[{"id":"https://openalex.org/I1289490764","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12","country_code":"US","type":"government","lineage":["https://openalex.org/I1289490764","https://openalex.org/I1299022934"]},{"id":"https://openalex.org/I35344726","display_name":"United States Public Health Service","ror":"https://ror.org/05xf94514","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I35344726"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alison Laufer Halpin","raw_affiliation_strings":["Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention , Atlanta, GA 30329, USA","U.S. Public Health Service , Rockville, MD 20852, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention , Atlanta, GA 30329, USA","institution_ids":["https://openalex.org/I1289490764"]},{"raw_affiliation_string":"U.S. Public Health Service , Rockville, MD 20852, USA","institution_ids":["https://openalex.org/I35344726"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020756463"],"corresponding_institution_ids":["https://openalex.org/I1289490764"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":null,"fwci":0.9787,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.71019108,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"38","issue":"2","first_page":"546","last_page":"548"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.1737000048160553,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.1737000048160553,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.13860000669956207,"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.10760000348091125,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/annotation","display_name":"Annotation","score":0.7763711810112},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6938308477401733},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5869418382644653},{"id":"https://openalex.org/keywords/virulence","display_name":"Virulence","score":0.4911136329174042},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.48964911699295044},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4717192053794861},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.447008341550827},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.4241040349006653},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3882670998573303},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37173956632614136}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7763711810112},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6938308477401733},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5869418382644653},{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.4911136329174042},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.48964911699295044},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4717192053794861},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.447008341550827},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.4241040349006653},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3882670998573303},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37173956632614136}],"mesh":[{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab607","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab607","pdf_url":null,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34415321","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34415321","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W2019385975","https://openalex.org/W2118688136","https://openalex.org/W2123981614","https://openalex.org/W2134852597","https://openalex.org/W2136145671","https://openalex.org/W2142678478","https://openalex.org/W2151831732","https://openalex.org/W2416070789","https://openalex.org/W2606367735","https://openalex.org/W2767753889","https://openalex.org/W2789546346","https://openalex.org/W2808824345","https://openalex.org/W2944755153","https://openalex.org/W2967125766","https://openalex.org/W3015086962","https://openalex.org/W4293196852","https://openalex.org/W6842402754"],"related_works":["https://openalex.org/W2114009169","https://openalex.org/W1979172052","https://openalex.org/W4205148382","https://openalex.org/W2194295138","https://openalex.org/W1506242385","https://openalex.org/W1972335439","https://openalex.org/W2049387417","https://openalex.org/W2148070420","https://openalex.org/W1577012645","https://openalex.org/W2027497088"],"abstract_inverted_index":{"MOTIVATION:":[0],"Tools":[1],"used":[2,140,166],"to":[3,24,34,91,167],"identify":[4],"genes":[5,124,151],"in":[6,26,50,59,152,177],"microbial":[7,178],"sequences":[8],"using":[9],"a":[10,17,101,126,189,195],"reference":[11],"database":[12,98],"generally":[13],"report":[14],"matches":[15,174],"as":[16,32,46,145,188,194],"percent":[18],"identity,":[19,31],"which":[20,58,86],"can":[21,38,61,137,164],"be":[22,139,165],"difficult":[23],"interpret":[25],"cases":[27],"with":[28,141],"<100%":[29],"sequence":[30],"changes":[33],"specific":[35],"amino":[36],"acids":[37],"have":[39,62],"dramatic":[40,63],"effects":[41,64],"on":[42,65],"protein":[43,88],"function,":[44],"such":[45],"when":[47],"they":[48],"occur":[49],"substrate":[51],"binding":[52],"regions":[53],"or":[54,70],"enzyme":[55],"active":[56],"sites,":[57],"turn":[60],"phenotypes":[66],"like":[67],"antimicrobial":[68,122],"resistance":[69,123],"virulence.":[71],"RESULTS:":[72],"Here,":[73],"we":[74,146],"present":[75],"GAMMA,":[76],"an":[77],"open-source":[78],"tool":[79],"for":[80,116],"Gene":[81],"Allele":[82],"Mutation":[83],"Microbial":[84],"Assessment,":[85],"uses":[87],"coding-level":[89],"identity":[90],"make":[92],"gene":[93,97,143,173],"calls":[94],"from":[95,125],"any":[96,142,172],"and":[99,106,161,170,193],"generates":[100],"classification":[102],"(e.g.":[103,109],"mutant,":[104],"truncation)":[105],"translated":[107],"annotation":[108],"Y190S":[110],"mutation,":[111],"truncation":[112],"at":[113,206],"residue":[114],"110)":[115],"these":[117],"calls.":[118],"GAMMA":[119,163,184],"accurately":[120],"called":[121],"large":[127],"set":[128],"of":[129,158,175],"genomes":[130],"faster":[131],"than":[132],"three":[133],"other":[134],"tools.":[135],"It":[136],"also":[138],"database,":[144],"demonstrated":[147],"by":[148],"identifying":[149],"virulence":[150],"the":[153],"same":[154],"genome":[155],"set.":[156],"Because":[157],"its":[159],"speed":[160],"flexibility,":[162],"rapidly":[168],"find":[169],"annotate":[171],"interest":[176],"sequencing":[179],"data.":[180],"AVAILABILITY":[181],"AND":[182],"IMPLEMENTATION:":[183],"is":[185],"freely":[186],"available":[187,205],"Bioconda":[190],"package":[191],"(https://bioconda.github.io/recipes/gamma/README.html)":[192],"command":[196],"line":[197],"script":[198],"(https://github.com/rastanton/GAMMA).":[199],"SUPPLEMENTARY":[200],"INFORMATION:":[201],"Supplementary":[202],"data":[203],"are":[204],"Bioinformatics":[207],"online.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
