SARG database

The SARG database also known as Structured Antibiotic Resistance Gene database is a collection of antimicrobial resistance genes.^[1] The hierarchical structure of the database is clear to be 1) Type: antibiotic type 2) Subtype: genotype 3) Sequence: reference sequence. The SARG database helps in quick survey of antimicrobial resistance genes from environmental samples.^[2]^[3] The database was initially integrated from ARDB and Comprehensive Antibiotic Resistance Database, followed by hand curation including removing non-ARG sequences, removing redundant sequences and SNP sequences.^[4] Other sources include NCBI nr database and published papers.

Online-analysis pipeline

References

^ Yin, Xiaole; Jiang, Xiao-Tao; Chai, Benli; Li, Liguan; Yang, Ying; Cole, James R; Tiedje, James M; Zhang, Tong (2018-07-01). Wren, Jonathan (ed.). "ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes". Bioinformatics. 34 (13): 2263–2270. doi:10.1093/bioinformatics/bty053. ISSN 1367-4803. PMID 29408954.
^ Murray, Aimee K.; Zhang, Lihong; Yin, Xiaole; Zhang, Tong; Buckling, Angus; Snape, Jason; Gaze, William H. (2018-07-24). Goldberg, Joanna B. (ed.). "Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities". mBio. 9 (4): e00969–18, /mbio/9/4/mBio.00969–18.atom. doi:10.1128/mBio.00969-18. ISSN 2150-7511. PMC 6058293. PMID 30042197.
^ Bürgmann, Helmut; Frigon, Dominic; H Gaze, William; M Manaia, Célia; Pruden, Amy; Singer, Andrew C.; F Smets, Barth; Zhang, Tong (2018-09-01). "Water and sanitation: an essential battlefront in the war on antimicrobial resistance". FEMS Microbiology Ecology. 94 (9). doi:10.1093/femsec/fiy101. ISSN 0168-6496. PMID 29878227.
^ Yang, Ying; Jiang, Xiaotao; Chai, Benli; Ma, Liping; Li, Bing; Zhang, Anni; Cole, James R.; Tiedje, James M.; Zhang, Tong (2016-08-01). "ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database". Bioinformatics. 32 (15): 2346–2351. doi:10.1093/bioinformatics/btw136. ISSN 1367-4803. PMID 27153579.

[1] Yin, Xiaole; Jiang, Xiao-Tao; Chai, Benli; Li, Liguan; Yang, Ying; Cole, James R; Tiedje, James M; Zhang, Tong (2018-07-01). Wren, Jonathan (ed.). "ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes". Bioinformatics. 34 (13): 2263–2270. doi:10.1093/bioinformatics/bty053. ISSN 1367-4803. PMID 29408954.

[2] Murray, Aimee K.; Zhang, Lihong; Yin, Xiaole; Zhang, Tong; Buckling, Angus; Snape, Jason; Gaze, William H. (2018-07-24). Goldberg, Joanna B. (ed.). "Novel Insights into Selection for Antibiotic Resistance in Complex Microbial Communities". mBio. 9 (4): e00969–18, /mbio/9/4/mBio.00969–18.atom. doi:10.1128/mBio.00969-18. ISSN 2150-7511. PMC 6058293. PMID 30042197.

[3] Bürgmann, Helmut; Frigon, Dominic; H Gaze, William; M Manaia, Célia; Pruden, Amy; Singer, Andrew C.; F Smets, Barth; Zhang, Tong (2018-09-01). "Water and sanitation: an essential battlefront in the war on antimicrobial resistance". FEMS Microbiology Ecology. 94 (9). doi:10.1093/femsec/fiy101. ISSN 0168-6496. PMID 29878227.

[4] Yang, Ying; Jiang, Xiaotao; Chai, Benli; Ma, Liping; Li, Bing; Zhang, Anni; Cole, James R.; Tiedje, James M.; Zhang, Tong (2016-08-01). "ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database". Bioinformatics. 32 (15): 2346–2351. doi:10.1093/bioinformatics/btw136. ISSN 1367-4803. PMID 27153579.

[1]

[2]

[3]

[4]

See also

References