PATRIC

ORGANISMS

Bacterial Pathogens

Acinetobacter Francisella

Bacillus Helicobacter

Bartonella Listeria

Borreliella Mycobacterium

Brucella Pseudomonas

Burkholderia Rickettsia

Campylobacter Salmonella

Chlamydia Shigella

Clostridium Staphylococcus

Coxiella Streptococcus

Ehrlichia Vibrio

Escherichia Yersinia

All Bacteria All Archaea Eukaryotic Hosts

DATA

Data Types

Antibiotic Resistance

Genomic Features

Protein Families

Specialty Genes

Transcriptomics

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FTP Server

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PATRIC Collaborations

NIAID Clinical Proteomics

NIAID Genome Sequencing

NIAID Structural Genomics

NIAID Systems Biology

NIAID Functional Genomics

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SERVICES

Genomics

Similar Genome Finder

Variation Analysis

Tn-Seq Analysis

Phylogenetic Tree

Transcriptomics

Expression Import

RNA-Seq Analysis

Protein Tools

Protein Family Sorter

Proteome Comparison

Metabolomics

Comparative Pathway

Model Reconstruction

Data

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New Services and Data

Recent Release

Phylogenetic Tree Builder constructs custom phylogenetic trees using conserved protein sequences.
Tn-Seq Analysis aligns reads and measures essentiality of Tn-seq data using the TRANSIT software.
Similar Genome Finder finds the closest related genomes to selected genome or FASTA file using MInHash.
Compare Region Viewer displays flanking regions of user selected genomes for a particular gene.
AMR Phenotype Data provides AMR phenotype and measurement method for list of genomes.
Antibiotic Database provides antibiotic name, description, chemical structure, mechanism, and pharmacology.

More Information

PATRIC Crosses 100,000 Genomes Mark

In the May 2017 release, PATRIC has added over 7,700 new genomes, bringing the total number of public genomes in PATRIC to approximately 105,000. This is a notable milestone for the project considering that the database contained only 400 bacterial genomes at the end of 2009 when PATRIC launched the all bacteria Bioinformatics Resource Center. The full list of available bacterial genomes can be accessed from the Genomes Tab for all bacteria in the PATRIC website.

More Information

Antibiotic Resistance Data

for Infectious Disease Research

Antibiotic Resistance refers to the ability of bacteria to develop resistance to antibiotics through gene mutation or acquisition of antibiotic resistance genes. PATRIC collects known antibiotic resistance genes from reputed external databases and publications and maps them to homologous genes using BLASTP, so you can easily find and analyze them with PATRIC tools. We also incorporate antibiotic susceptibility testing results as additional genome metadata.

Supporting the TB Research Community

THROUGH NEW TB@PATRIC RESOURCES

PATRIC announces new web-based features designed to serve TB researchers worldwide. This resource provides fast searching and powerful comparative analysis tools for all Mycobacterium tuberculosis genomes, including the H37Rv reference genome, its variants and other members in the tuberculosis complex. Also included are important reference genomes, M. smegmatis and M. marinum.

Visit TB@PATRIC

New Services & Data

In PATRIC

100,000 Genomes

In PATRIC

INVESTIGATING

ANTIBIOTIC RESISTANCE

SUPPORTING

THE TB COMMUNITY

Browse Data

GENOMES
GENOMIC FEATURES
SPECIALTY GENES
PROTEIN FAMILIES
PATHWAYS
TRANSCRIPTOMICS

What Can I Do @ PATRIC?

Genome Assembly

The Genome Assembly Service App can be used to perform an automatic genome assembly using the latest computational tools. Single or multiple assemblers can be invoked to compare results. Note: You must have a PATRIC user account and be logged in to use this service.
Protein Family Sorter

Compares protein families across closely related or diverse groups of genomes, visualizes them using interactive heatmaps, and generates multiple sequence alignments and phylogenetic trees for individual families. The heatmap view is an interactive visualization tool that provides an overview of the distribution of proteins across a selected set of genomes.
Genome Metadata

Supports searching for and locating genomes of interest based on various combinations of 61 different metadata fields. For instance, all genomes that have been isolated from humans, genomes related by phylogeny, or genomes related by lifestyle.

Genome Annotation

The Genome Annotation Service is a fully-automated pipeline for annotating bacterial and archaeal genomes using RAST (Rapid Annotation using Subsystem Technology) to provide high quality genome annotations. Note: You must have a PATRIC user account and be logged in to use this service.
Comparative Pathway Tool

Supports comparison of consistently annotated metabolic pathways across closely related or diverse groups of genomes and visualizes them using interactive KEGG maps and heatmaps. The heatmap view is an interactive visualization tool that provides an overview of the distribution of genomes across the set of EC numbers within a selected pathway.
Gene Page Transcriptomics

Summarizes all comparisons in which a gene is differentially expressed and associated metadata such as Strain, Gene Modification, and Experimental Condition. Expression value based filters and metadata graphical summaries enable quick discovery of top experimental conditions and gene manipulations related to the differential expression of the gene. Note: Links to example Gene Page for VBIMycTub87468_2933.

Recent News

7/31/2017

PATRIC July 2017 Release Features over 3900 New Genomes, and New Functionality and Data Including a New Phylogenetic Tree Building Service and Enhancements to Multiple Services and Tools.

PATRIC July 2017 Data and Website Release: Data Updates: New Genomes In this release, PATRIC has added 3902 new genomes and associated metadata, bringing the total number of genomes in PATRIC to over 108,000. The full list of available bacterial genomes can be accessed from the Genomes Tab for all bacteria, and from the Genomes Data Landing […]

6/9/2017

PATRIC/RAST Workshop at Argonne National Laboratory, August 14-16, 2017

The PATRIC/RAST workshop being offered on 2017 August 14-16 is now FULL. We thank all those who have enquired for their kind interest in PATRIC and RAST. We will post information regarding the date and location of the next workshop as soon as it scheduled. The PATRIC/RAST teams will be offering a tutorial on 2017-August […]

5/31/2017

PATRIC May 2017 Release brings total genomes to over 100,000 and includes 21 host response data sets

New Genomes In this release, PATRIC has added over 7,700 new genomes, bringing the total number of public genomes in PATRIC to 103,779 bacterial, 1,078 archeal, and 10 eukaryotic host. This is a notable milestone for the project, especially considering that the database contained only 400 bacterial genomes at the end of 2009, when PATRIC […]

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