抗性基因數(shù)據(jù)庫(kù)（1）
宏基因組：
檢測(cè)細(xì)菌猖败、病毒等序列
耐藥基因：
檢測(cè)檢出非人序列中的已知耐藥基因辽聊，找到對(duì)應(yīng)耐藥基因的抗生素
耐藥/抗性基因數(shù)據(jù)庫(kù)
- ARDB（Antibiotic Resistance Genes Database）數(shù)據(jù)庫(kù)努潘。整合了來(lái)自NCBI和SwissProt數(shù)據(jù)庫(kù)的13,254個(gè)耐藥基因信息授帕，經(jīng)過(guò)數(shù)據(jù)過(guò)濾和去重后鹏倘，保留4,554個(gè)完整非冗余的耐藥蛋白數(shù)據(jù)。這些蛋白數(shù)據(jù)和GO嘹害、CDD撮竿、COG吮便、物種信息等數(shù)據(jù)整合笔呀，并根據(jù)耐藥機(jī)制進(jìn)行歸類(lèi)。
- CARD數(shù)據(jù)庫(kù)(http://arpcard.mcmaster.ca)基于志愿者貢獻(xiàn)的數(shù)據(jù)共享平臺(tái)髓需，以ARO（Antibiotic Resistance Ontology）為核心對(duì)抗性數(shù)據(jù)進(jìn)行組織许师，達(dá)到數(shù)據(jù)實(shí)時(shí)更新的效果。
- ResFams以CARD的抗藥基因數(shù)據(jù)為核心僚匆，結(jié)合已有多個(gè)抗藥基因數(shù)據(jù)庫(kù)構(gòu)建了HMM模型微渠，以提升抗藥基因預(yù)測(cè)效果。
- ARDB不再維護(hù)咧擂，其數(shù)據(jù)在CARD中收錄并維護(hù)
- ARDB提供命令線版本的抗性基因注釋工具ardbAnno
- CARD RGI工具
- 輸入文件可以是微生物的基因組序列逞盆、組裝序列和蛋白質(zhì)序列
- heatmap圖
- bwt（bwa and bowtie2）算法（unpublished algorithm undergoing beta-testing），輸入直接為宏基因組的fastq
輸出如下：
Reference Sequence ARO Term ARO Accession Reference Model Type Reference DB Reference Allele Source Resistomes & Variants: Observed in Genome(s) Resistomes & Variants: Observed in Plasmid(s) Resistomes & Variants: Observed Pathogen(s) Completely Mapped Reads Mapped Reads with Flanking Sequence All Mapped Reads Percent Coverage Length Coverage (bp) Average MAPQ (Completely Mapped Reads) Mate Pair Linkage Reference Length AMR Gene Family Drug Class Resistance Mechanism
ARO:3000567|ID:945|Name:tet(40)|NCBI:AM419751 tet(40) 3000567 protein homolog model CARD CARD curation no data no data uncultured bacterium 2 0 2 20.07 245 60.00 1221 major facilitator superfamily (MFS) antibiotic efflux pump tetracycline antibiotic antibiotic efflux
ARO:3000191|ID:1183|Name:tetQ|NCBI:Z21523 tetQ 3000191 protein homolog model CARD CARD curation no data no data Bacteroides fragilis 10 0 10 69.35 1369 60.00 1974 tetracycline-resistant ribosomal protection protein tetracycline antibiotic antibiotic target protection
ARO:3000190|ID:2020|Name:tetO|NCBI:M18896.2 tetO 3000190 protein homolog model CARD CARD curation no data no data Campylobacter jejuni 2 0 2 26.09 501 60.00 1920 tetracycline-resistant ribosomal protection protein tetracycline antibiotic antibiotic target protection
ARO:3004454|ID:2893|Name:Campylobacter_coli_chloramphenicol_acetyltransferase|NCBI:M35190.1 Campylobacter coli chloramphenicol acetyltransferase 3004454 protein homolog model CARD CARD curation no data no data Campylobacter coli 2 0 2 25.96 162 60.00 624 chloramphenicol acetyltransferase (CAT) phenicol antibiotic antibiotic inactivation
