The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4).
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4).
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DOI：
10.1186/s40793-016-0138-x
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发表时间：
2016
影响因子：
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通讯作者：
Kyrpides NC
中科院分区：
文献类型：
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作者：
Huntemann M;Ivanova NN;Mavromatis K;Tripp HJ;Paez-Espino D;Tennessen K;Palaniappan K;Szeto E;Pillay M;Chen IM;Pati A;Nielsen T;Markowitz VM;Kyrpides NC
DOE-JGI 宏基因组注释管道 (MAP v.4) 对宏基因组序列进行结构和功能注释，这些序列提交给微生物组集成微生物基因组 (IMG/M) 系统进行比较分析。该管道在通过 IMG 提交网站提供的核苷酸序列上运行。用户必须首先在 GOLD 中定义其分析项目，然后以 fasta 和 fastq 文件格式提交由支架/重叠群组成的相关序列数据集，以及可选的覆盖信息和/或未组装的读数。 MAP 处理包括特征预测，包括蛋白质编码基因、非编码 RNA 和调节 RNA 以及 CRISPR 元件的识别。结构注释之后是功能注释，包括蛋白质产品名称的分配以及与各种蛋白质家族数据库的连接。
The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation is followed by functional annotation including assignment of protein product names and connection to various protein family databases.