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Table 2 Public databases and software programs integrated in PHIDIAS

From: PHIDIAS: a pathogen-host interaction data integration and analysis system

Databases

  

Resources

Databases and analysis programs

Comments

   NCBI

RefSeq

Reference sequences

 

Genome

Genome summary

 

Gene

Gene information

 

Protein

Protein information

 

Nucleotide

Nucleotide information

 

CDD

Conserved domains

 

COGs

Clusters of orthologous groups

 

Taxonomy

Brucella taxonomy information

 

PubMed

Biomedical publications

 

GEO

Gene expression database

   EBI and SIB

ArrayExpress

Gene expression database

 

Swissprot

Annotated protein data

 

TrEMBL

Protein data

 

InterPro

Protein families, domains and functions

 

PROSITE

Protein families and domains

   VBI

PathInfo

PIML documents via web service

 

MiNet

MiNetML documents via web service

   TIGR

CMR

Comprehensive microbial resource

 

TIGRfam

TIGRfam assignments

 

GO

Gene ontology

 

KEGG

Pathways

 

BioCyc

Biological pathways

 

PFam

Protein domains and families

 

ProDom

Protein domain families

 

PDB

Protein database

   University of Michigan

BBP

Brucella bioinformatics portal

 

HazARD

Hazards in animal research database

Software programs integrated

  

   NCBI

BLAST

Blastn, blastp, blastx, tblastn, tblastx, PSI/PHI Blast, Mega Blast, Blast 2 sequences

   GMOD

GBrowse

Genome browsing and analysis

 

BioPerl

Programming tools

 

BioPAX

Biological pathway data exchange format

  1. CMR, TIGR Comprehensive Microbial Resource; GO, Gene Ontology; MeSH, Medical Subject Headings; PDB, Protein Data Bank.