Dandekar & Chandler:Useful websites

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Pseudomonas-specific websites

Pseudomonas Genome DB

- Best starting place for gene lookup
- Automatically set to PAO1 as reference genome
- Search by gene name, locus tag, or by coordinates
- Easily see gene neighborhood and get sequences, including 500 bp upstream and downstream
- Link out to Pseudomonas Ortholog Database
- Very excellent link out to JBrowse, which will show all in once place:
  • Functional Domain Predictions
  • Gene and Protein Annotations
  • Genomic Island Predictions
  • Regulatory Regions
- Very excellent link out to PseudoCyc Metabolic Pathways

Prokaryotic Genome Analysis Tool (PGAT) - UW Genomics

- Repository for UW-sequenced projects (including some EPIC strains)
- Must login through UW to access in progress and lab-specific sequencing

JGI - Integrated Microbial Genomes (IMG)