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Protocols

PATRIC specifications

Information


Unique identifier OMICS_01658
Name PATRIC
Alternative name Pathosystems Resource Integration Center
Restrictions to use None
Data access File download, Browse
Version 3.3.18
Maintained Yes

Subtool


  • NMPDR

Maintainers


  • person_outline Alice R. Wattam
  • person_outline Jeremy D. Glasner
  • person_outline James Davis

Additional information


User Guide: https://www.patricbrc.org/public/video/P3_QUICKSTART_V2.mp4

Publications for Pathosystems Resource Integration Center

PATRIC citations

 (206)
call_split

Complete Genome Sequences of 10 Yersinia pseudotuberculosis Isolates Recovered from Wild Boars in Germany

2018
Genome Announc
PMCID: 5946050
PMID: 29748399
DOI: 10.1128/genomeA.00266-18
call_split See protocol

[…] sequencer (Illumina, San Diego, CA, USA). Sequencing libraries were conducted using the Illumina Nextera XT DNA sample preparation kit. Raw read data were used for de novo genome assembling using the PATRIC database (https://patricbrc.org) (). SPAdes assembly calculations resulted in 10- to 20-fold sequence coverages per consensus sequence for all isolates. Genome annotation using the automated Pr […]

library_books

A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars

2018
Front Microbiol
PMCID: 5934430
PMID: 29755434
DOI: 10.3389/fmicb.2018.00805

[…] e genes were searched by BLASTn analysis with default parameters using the Virulence Factors of Pathogenic Bacteria Database (VFDB) (Chen et al., ), Victors Database (University of Michigan, USA) and PATRIC_VF (Wattam et al., ). Antibiotic resistance genes were searched using the Antibiotic Resistance Database (ARDB) (Liu and Pop, ) and the Comprehensive Antibiotic Resistance Database (CARD) (Jia […]

library_books

Draft Genome Sequence of the Extremely Desiccation Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1

2018
Genome Announc
PMCID: 5920166
PMID: 29700137
DOI: 10.1128/genomeA.00216-18

[…] contigs. Finally, gene prediction and annotation of the Gloeocapsopsis sp. AAB1 contigs were carried out using the Rapid Annotations using Subsystems Technology (RAST) pipeline () as provided by the Pathosystems Resource Integration Center (PATRIC) server (). A total of 5,641 coding DNA sequences (CDSs), 38 tRNA genes, and 5 rRNA genes were identified. […]

library_books

Elucidation of the anti hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

2018
BMC Genomics
PMCID: 5918772
PMID: 29695242
DOI: 10.1186/s12864-018-4672-3

[…] for motif analysis. Stringent parameters were used to identify tRNAs by trnascan-se [] and ribosomal binding sites by RBSfinder. After resequencing, the Genome atlas was generated by Geneious 5.5 and PATRIC []. Prophage regions within the genome were identified using PHAST. Whole-genome nucleotide alignments were generated and visualized by Mauve. Identification of core genes and unique genes was […]

library_books

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino Oligosaccharide Utilization

2018
Front Microbiol
PMCID: 5928203
PMID: 29740413
DOI: 10.3389/fmicb.2018.00776

[…] s, Geodermatophilus obscurus, and Stackebrandtia nassauensis. The whole-genome phylogeny tree for the selected Bifidobacteriaceae genomes was build using the Phylogenetic Tree service included in the PATRIC genomic platform (). Phylogenetic trees for the selected protein families were constructed via the PhyML algorithm () in the Seaview software (), using the default parameters and bootstrap valu […]

library_books

Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence

2018
Front Microbiol
PMCID: 5932413
PMID: 29755430
DOI: 10.3389/fmicb.2018.00782

[…] NCBI taxonomy identifiers were mined in the genome metadata sourced from PATRIC through text matching of proteome IDs and organism IDs, respectively, which were later used for constructing a phylogenetic tree via phyloT in order to investigate distribution patterns of poly […]

Citations

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PATRIC institution(s)
Biosciences Division at Argonne National Laboratory, University of Chicago Department of Medicine, IL, USA; Department of Computer Science, University of Chicago, IL, USA; e Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt; Computing, Environmental and Biological Sciences Directorate at Argonne National Laboratory, IL, USA; Fellowship for Interpretation of Genomes, IL, USA; Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA; University of Illinois at Urbana-Champaign, IL, USA; Computation Institute, University of Chicago, IL, USA; Computing, Environment and Life Sciences Division, Argonne National Laboratory, IL, USA
PATRIC funding source(s)
Supported by The NIAID, National Institutes of Health, Department of Health and Human Services (grant number HHSN272201400027C).

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