Acknowledgements

This page lists the data sources and third party software tools used in PATRIC. Click here for a list of PATRIC joint publications with other Scientific Collaborators.

Data Sources Used by PATRIC

ARDB (Antibiotic Resistance Genes Database)

BIND (Berkeley Internet Name Domain)

BioGRID (Biological General Repository for Interaction Datasets)

CARD (The Comprehensive Antibiotic Resistance Database)

CTD (Comparative Toxicogenomics Database)

DIP (Database of Interacting Proteins)

DrugBank

EBI (European Bioinformatics Institute)

• ArrayExpress

• PRIDE

• IntAct

GAD (Genetic Association Database)

GO (Gene Ontology)

HealthMap

HMP (Human Microbiome Project)

IEDB (Immune Epitope Database)

KEGG (Kyoto Encyclopedia of Genes and Genomes)

MINT (Molecular Interaction Database)

NCBI (National Center for Biotechnology Information)

• BioProject

• CDD

• Genome

• GEO

• MMDB

• PubMed

• RefSeq

• Taxonomy

PDB (Protein Data Bank)

PSICQUIC (Protemics Standard Initiative Common Query Interface)

STITCH (Search Tool for Interactions of Chemicals)

STRING (Search Tool for the Retrieval of Interacting Genes/Proteins)

TTD (Therapeutic Targets Database)

UniProt (Universal Protein Resource)

Victors Virulence Factors

VFDB (Virulence Factors Database)

Software and Tools used by PATRIC

BLAST (Basic Local Alignment Search Tool)

BLAT

Circos

Cluster3

Cytoscape

FastTree

Gblocks

HMMER

JBrowse via The Holmes Lab

Jmol

MCL (Markov Cluster Algorithm)

MUSCLE (Multiple Sequence Comparison by Log- Expectation)

OrthoMCL

PATRIC Data Release Policy