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Title: The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.
Authors:
 [1] ;  [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [2] ;  [2] ;  [2] ;  [1] ;  [1] ;  [2] ;  [1]
  1. DOE Joint Genome Inst., Walnut Creek, CA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Microbial Genome Annotation; SOP; IMG; JGI
OSTI Identifier:
1256940
Alternate Identifier(s):
OSTI ID: 1378607

Huntemann, Marcel, Ivanova, Natalia N., Mavromatis, Konstantinos, Tripp, H. James, Paez-Espino, David, Palaniappan, Krishnaveni, Szeto, Ernest, Pillay, Manoj, Chen, I-Min A., Pati, Amrita, Nielsen, Torben, Markowitz, Victor M., and Kyrpides, Nikos C.. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). United States: N. p., Web. doi:10.1186/s40793-015-0077-y.
Huntemann, Marcel, Ivanova, Natalia N., Mavromatis, Konstantinos, Tripp, H. James, Paez-Espino, David, Palaniappan, Krishnaveni, Szeto, Ernest, Pillay, Manoj, Chen, I-Min A., Pati, Amrita, Nielsen, Torben, Markowitz, Victor M., & Kyrpides, Nikos C.. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). United States. doi:10.1186/s40793-015-0077-y.
Huntemann, Marcel, Ivanova, Natalia N., Mavromatis, Konstantinos, Tripp, H. James, Paez-Espino, David, Palaniappan, Krishnaveni, Szeto, Ernest, Pillay, Manoj, Chen, I-Min A., Pati, Amrita, Nielsen, Torben, Markowitz, Victor M., and Kyrpides, Nikos C.. 2015. "The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)". United States. doi:10.1186/s40793-015-0077-y. https://www.osti.gov/servlets/purl/1256940.
@article{osti_1256940,
title = {The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)},
author = {Huntemann, Marcel and Ivanova, Natalia N. and Mavromatis, Konstantinos and Tripp, H. James and Paez-Espino, David and Palaniappan, Krishnaveni and Szeto, Ernest and Pillay, Manoj and Chen, I-Min A. and Pati, Amrita and Nielsen, Torben and Markowitz, Victor M. and Kyrpides, Nikos C.},
abstractNote = {The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.},
doi = {10.1186/s40793-015-0077-y},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 10,
place = {United States},
year = {2015},
month = {10}
}

Works referenced in this record:

Search and clustering orders of magnitude faster than BLAST
journal, August 2010