The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

Marcel Huntemann; Natalia N. Ivanova; Konstantinos Mavromatis; H. James Tripp; David Paez-Espino; Kristin Tennessen; Krishnaveni Palaniappan; Ernest Szeto; Manoj Pillay; I-Min A. Chen; Amrita Pati; Torben Nielsen; Victor M. Markowitz; Nikos C. Kyrpides

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The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

机译：DOE-JGI元基因组注释管道的标准操作程序（MAP v.4）

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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.

机译：DOE-JGI元基因组注释管道（MAP v.4）对宏基因组序列执行结构和功能注释，这些宏基因组序列已提交给带有微生物群落的集成微生物基因组（IMG / M）系统进行比较分析。管道在通过IMG提交站点提供的核苷酸序列上运行。用户必须首先以GOLD定义其分析项目，然后提交相关的序列数据集，该序列数据集由脚手架/重叠群组成，具有可选的覆盖率信息和/或以fasta和fastq文件格式进行未汇编的读取。 MAP处理包括特征预测，包括蛋白质编码基因，非编码RNA和调控RNA以及CRISPR元件的鉴定。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。

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《Standards in Genomic Sciences》 |2016年第1期|共页
作者
Marcel Huntemann; Natalia N. Ivanova; Konstantinos Mavromatis; H. James Tripp; David Paez-Espino; Kristin Tennessen; Krishnaveni Palaniappan; Ernest Szeto; Manoj Pillay; I-Min A. Chen; Amrita Pati; Torben Nielsen; Victor M. Markowitz; Nikos C. Kyrpides;
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中图分类遗传学;
关键词
Metagenome annotationSOPIMGJGI;

机译：元基因组注释;

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6. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) [O] . Marcel Huntemann, Natalia N. Ivanova, Konstantinos Mavromatis, 2016

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7. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) [O] . Marcel Huntemann, Natalia N. Ivanova, Konstantinos Mavromatis, 2016

机译：DOE-JGI元基因组注释管道的标准操作程序（MAP v.4）

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

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