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NMPDR specifications


Unique identifier OMICS_21115
Alternative name National Microbial Pathogen Data Resource
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • Functional Clusters
  • Signature Genes


  • person_outline Team NGS catalog
  • person_outline Leslie Klis McNeil

Additional information


Publication for National Microbial Pathogen Data Resource

NMPDR citations


Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype

Sci Rep
PMCID: 5928088
PMID: 29712985
DOI: 10.1038/s41598-018-25233-x
call_split See protocol

[…] nce of the Stx converting phage was extracted from the complete genome by using the PHASTER (http://phaster.ca/), the genome of Stx converting phage was reannotated using the RAST server (http://rast.nmpdr.org/), and then manually verified and corrected. Functional annotation of selected CDSs was performed based on the results of homology searches against the public nonredundant protein database ( […]


Dissemination of blaNDM 5 gene via an IncX3 type plasmid among non clonal Escherichia coli in China

PMCID: 5918551
PMID: 29713466
DOI: 10.1186/s13756-018-0349-6

[…] representative plasmid were closed by standard PCR and Sanger sequencing according to previous study []. The RAST (Rapid Annotation using Subsystems Technology) annotation website server (http://rast.nmpdr.org/rast.cgi) was then used to annotate the genomes of the plasmid. The circular map of the pEC463-NDM5 plasmid was generated using the CGview server []. A comparison of pEC463-NDM5 and three re […]


Draft Genome Sequence of Plant Growth Promoting Burkholderia sp. Strain BE12, Isolated from the Rhizosphere of Maize

Genome Announc
PMCID: 5920190
PMID: 29700147
DOI: 10.1128/genomeA.00299-18
call_split See protocol

[…] des 97 contigs with a GC content of 66.94% and an N50 contig size of 180,386 bp. Gene function prediction was performed by the Rapid Annotations using Subsystems Technology (RAST) server (http://rast.nmpdr.org) () followed by an annotation using the SEED database (), resulting in 71 RNAs and 7,040 coding sequences.In silico analysis using antiSMASH () and RAST revealed the presence of a siderophor […]


Draft Genome Sequences of Five Staphylococcus aureus Strains Isolated from Clinically Healthy Cows in the Russian Federation

Genome Announc
PMCID: 5908943
PMID: 29674545
DOI: 10.1128/genomeA.00275-18
call_split See protocol

[…] zes ranged from 2.69 to 2.73 Mb. Each genome contains 2,796 to 2,855 genes. The assembled contigs were annotated using the Rapid Annotation using Subsystem Technology (RAST) v.2.0 server (http://rast.nmpdr.org) () and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP; https://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). In genotyping analysis, S. aureus strain 17 was classified as seque […]


Gene expression and ultrastructure of meso‐ and thermophilic methanotrophic consortia

Environ Microbiol
PMCID: 5947290
PMID: 29468803
DOI: 10.1111/1462-2920.14077

[…] sembly quality and bin completeness was assessed using Quast (Gurevich et al., ) and CheckM (Parks et al., ). Draft genomes were automatically annotated using Prokka (Seemann, ) and RAST (http://rast.nmpdr.org/). Additionally, protein domains were identified by Hmmscan (Eddy, 2011) against the PfamA (database release 30; Punta et al., 2012) and TIGRFAM (database release 15; Haft et al., ) database […]


In vitro studies of Rickettsia host cell interactions: Confocal laser scanning microscopy of Rickettsia helvetica infected eukaryotic cell lines

PLoS Negl Trop Dis
PMCID: 5825168
PMID: 29432420
DOI: 10.1371/journal.pntd.0006151
call_split See protocol

[…] On average, the coverage of the R. helvetica AS819 plasmid was 146-fold and the coverage of the genome was 34-fold. We predicted CDSs using the RAST prokaryotic genome annotation server (http://rast.nmpdr.org/rast). RNAs were identified using tRNAscan-SE v. 1.23 (tRNA), aragorn v. 1.2.34 (tRNA, tmRNA), and RNammer v.2.1 (rRNA). Database searches were done using BLAST and infernal. Hereby sca2 gen […]

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NMPDR institution(s)
National Center for Supercomputing Applications and; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Microbiology and Immunology, College of Pharmacy, Cairo University, Cairo, Egypt; Computation Institute, University of Chicago, Chicago, IL, USA; Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA; San Diego State University, San Diego, CA, USA; The Burnham Institute, San Diego, CA, USA; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA; Biomedical Research Centre, University of Dundee, Dundee, UK
NMPDR funding source(s)
Supported by Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN266200400042C.

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