抗性基因数据库(1)

抗性基因数据库（1）

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宏基因组：
检测细菌、病毒等序列

耐药基因：
检测检出非人序列中的已知耐药基因，找到对应耐药基因的抗生素

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耐药/抗性基因数据库

1. ARDB（Antibiotic Resistance Genes Database）数据库。整合了来自NCBI和SwissProt数据库的13,254个耐药基因信息，经过数据过滤和去重后，保留4,554个完整非冗余的耐药蛋白数据。这些蛋白数据和GO、CDD、COG、物种信息等数据整合，并根据耐药机制进行归类。
2. CARD数据库(http://arpcard.mcmaster.ca)基于志愿者贡献的数据共享平台，以ARO（Antibiotic Resistance Ontology）为核心对抗性数据进行组织，达到数据实时更新的效果。
3. ResFams以CARD的抗药基因数据为核心，结合已有多个抗药基因数据库构建了HMM模型，以提升抗药基因预测效果。

• ARDB不再维护，其数据在CARD中收录并维护
• ARDB提供命令线版本的抗性基因注释工具ardbAnno
• CARD RGI工具
  • 输入文件可以是微生物的基因组序列、组装序列和蛋白质序列
  • heatmap图
  • bwt（bwa and bowtie2）算法（unpublished algorithm undergoing beta-testing），输入直接为宏基因组的fastq

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输出如下：

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