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Protocols

PAMDB specifications

Information


Unique identifier OMICS_23286
Name PAMDB
Alternative name Pseudomonas aeruginosa Metabolome Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.0
Maintained Yes

Maintainers


  • person_outline Angela Wilks
  • person_outline Amanda Oglesby-Sherrouse
  • person_outline Maureen Kane

Publication for Pseudomonas aeruginosa Metabolome Database

PAMDB citations

 (4)
library_books

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

2017
Nucleic Acids Res
PMCID: 5753253
PMID: 29316735
DOI: 10.1093/nar/gkx1235

[…] lease 4.0 brings huge increases in content, an improved interface and new kinds of information—predicted mass spectra and pharmacometabolomics. This issue also reports on a new metabolomics database, PAMDB (), devoted to the bacterial pathogen Pseudomonas aeruginosa, justified not only by the biomedical importance of the organism but also by the novel metabolites that it contains. Metabolic pathwa […]

call_split

Genomics enabled analysis of the emergent disease cotton bacterial blight

2017
PLoS Genet
PMCID: 5614658
PMID: 28910288
DOI: 10.1371/journal.pgen.1007003
call_split See protocol

[…] deposited on NCBI () [].Multi-locus sequence analysis was conducted by concatenating sequences of the gltA, lepA, lacF, gyrB, fusA and gap-1 loci obtained from the Plant-Associated Microbes Database (PAMDB) for each strain as previously described []. A maximum-likelihood tree using these concatenated sequences was generated using CLC Genomics 7.5. […]

call_split

A User's Guide to a Data Base of the Diversity of Pseudomonas syringae and Its Application to Classifying Strains in This Phylogenetic Complex

2014
PLoS One
PMCID: 4153583
PMID: 25184292
DOI: 10.1371/journal.pone.0105547
call_split See protocol

[…] gapA (glyceraldehyde-3-phosphate dehydrogenase A), rpoD (RNA polymerase sigma70 factor) and gyrB (gyrase B), using the Morris MLST schema of the Plant Associated and Environmental Microbes Database (PAMDB, http://genome.ppws.vt.edu/cgi-bin/MLST/home.pl) in combination with gapA and gyrB of the Hwang PAMDB schema , . For each locus, sequences were extracted from GenBank and PAMDB, aligned with the […]

library_books

Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

2011
BMC Genomics
PMCID: 3071791
PMID: 21396108
DOI: 10.1186/1471-2164-12-146

[…] MLST sequences (fusA, gapA, gltA, gyrB, lacF, lepA) for all the genomes were obtained in concatenated form from PAMDB website http://pamdb.org. Genes and their corresponding amino acid sequences spanning gum, hrp cluster were downloaded from NCBI genbank sequences of sequenced genomes. Amino acid sequences of p […]

Citations

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PAMDB institution(s)
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA; Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
PAMDB funding source(s)
Supported by National Institutes of Health [AI102883; AI123320; HD077260]; University of Maryland, School of Pharmacy, Mass Spectrometry Center [SOP1841- IQB2014]; Genome Canada and the Canadian Institutes of Health Research.

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