The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)
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 provide d 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.
- Research Organization:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Grant/Contract Number:
- AC02-05CH11231
- OSTI ID:
- 1618964
- Alternate ID(s):
- OSTI ID: 1379106
- Journal Information:
- Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Vol. 11 Journal Issue: 1; ISSN 1944-3277
- Publisher:
- Springer Science + Business MediaCopyright Statement
- Country of Publication:
- United Kingdom
- Language:
- English
Web of Science
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The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
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