The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
Abstract
© 2016 Huntemann et al. 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. Structural annotation is followed by assignment of protein product names and functions.
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618953
- Alternate Identifier(s):
- OSTI ID: 1256940; OSTI ID: 1378607
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Standards in Genomic Sciences
- Additional Journal Information:
- Journal Name: Standards in Genomic Sciences Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 1944-3277
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Microbial Genome Annotation; SOP; IMG; JGI
Citation Formats
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 Kingdom: N. p., 2015.
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 Kingdom. https://doi.org/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. Mon .
"The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)". United Kingdom. https://doi.org/10.1186/s40793-015-0077-y.
@article{osti_1618953,
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 = {© 2016 Huntemann et al. 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. 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 Kingdom},
year = {Mon Oct 26 00:00:00 EDT 2015},
month = {Mon Oct 26 00:00:00 EDT 2015}
}
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https://doi.org/10.1186/s40793-015-0077-y
https://doi.org/10.1186/s40793-015-0077-y
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