Open Access
Nucleic Acids Research, volume 45, issue D1, pages D535-D542
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
Wattam Alice R
,
Davis James J.
,
Assaf Rida
,
Boisvert Sébastien
,
Brettin Thomas
,
Bun Christopher
,
Conrad Neal
,
Dietrich Emily M
,
Disz Terry
,
Gabbard Joseph L.
,
Gerdes Svetlana
,
Henry Christopher S.
,
Kenyon Ronald W
,
Machi Dustin
,
Mao Chunhong
,
Nordberg Eric K.
,
Olsen Gary J.
,
Murphy Olson Daniel E
,
Olson Robert
,
Overbeek Ross
,
Parrello Bruce
,
Pusch Gordon D
,
Shukla Maulik
,
Vonstein Veronika
,
Warren Andrew
,
Xia Fangfang
,
Yoo Hyunseung
,
Stevens Rick L.
Publication type: Journal Article
Publication date: 2016-11-29
Journal:
Nucleic Acids Research
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 14.9
ISSN: 03051048, 13624962
PubMed ID:
27899627
Genetics
Abstract
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by ‘virtual integration’ to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Wattam A. R. et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center // Nucleic Acids Research. 2016. Vol. 45. No. D1. p. D535-D542.
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Wattam A. R., Davis J. J., Assaf R., Boisvert S., Brettin T., Bun C., Conrad N., Dietrich E. M., Disz T., Gabbard J. L., Gerdes S., Henry C. S., Kenyon R. W., Machi D., Mao C., Nordberg E. K., Olsen G. J., Murphy Olson D. E., Olson R., Overbeek R., Parrello B., Pusch G. D., Shukla M., Vonstein V., Warren A., Xia F., Yoo H., Stevens R. L. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center // Nucleic Acids Research. 2016. Vol. 45. No. D1. p. D535-D542.
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TY - JOUR
DO - 10.1093/nar/gkw1017
UR - https://doi.org/10.1093%2Fnar%2Fgkw1017
TI - Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
T2 - Nucleic Acids Research
AU - Wattam, Alice R
AU - Davis, James J.
AU - Assaf, Rida
AU - Boisvert, Sébastien
AU - Brettin, Thomas
AU - Bun, Christopher
AU - Conrad, Neal
AU - Dietrich, Emily M
AU - Disz, Terry
AU - Gabbard, Joseph L.
AU - Gerdes, Svetlana
AU - Henry, Christopher S.
AU - Kenyon, Ronald W
AU - Machi, Dustin
AU - Mao, Chunhong
AU - Nordberg, Eric K.
AU - Olsen, Gary J.
AU - Murphy Olson, Daniel E
AU - Olson, Robert
AU - Overbeek, Ross
AU - Parrello, Bruce
AU - Pusch, Gordon D
AU - Shukla, Maulik
AU - Vonstein, Veronika
AU - Warren, Andrew
AU - Xia, Fangfang
AU - Yoo, Hyunseung
AU - Stevens, Rick L.
PY - 2016
DA - 2016/11/29 00:00:00
PB - Oxford University Press
SP - D535-D542
IS - D1
VL - 45
PMID - 27899627
SN - 0305-1048
SN - 1362-4962
ER -
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@article{2016_Wattam,
author = {Alice R Wattam and James J. Davis and Rida Assaf and Sébastien Boisvert and Thomas Brettin and Christopher Bun and Neal Conrad and Emily M Dietrich and Terry Disz and Joseph L. Gabbard and Svetlana Gerdes and Christopher S. Henry and Ronald W Kenyon and Dustin Machi and Chunhong Mao and Eric K. Nordberg and Gary J. Olsen and Daniel E Murphy Olson and Robert Olson and Ross Overbeek and Bruce Parrello and Gordon D Pusch and Maulik Shukla and Veronika Vonstein and Andrew Warren and Fangfang Xia and Hyunseung Yoo and Rick L. Stevens},
title = {Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center},
journal = {Nucleic Acids Research},
year = {2016},
volume = {45},
publisher = {Oxford University Press},
month = {nov},
url = {https://doi.org/10.1093%2Fnar%2Fgkw1017},
number = {D1},
pages = {D535--D542},
doi = {10.1093/nar/gkw1017}
}
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Wattam, Alice R., et al. “Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.” Nucleic Acids Research, vol. 45, no. D1, Nov. 2016, pp. D535-D542. https://doi.org/10.1093%2Fnar%2Fgkw1017.