PseudoCAP: Tools

!doctype html public "-//w3c//dtd html 4.0 transitional//en"> PseudoCAP: Tools

Tools for
Pseudomonas aeruginosa
genome analysis and
annotation resources

If you have a suggestion for information that should be added here, please contact the PseudoCAP moderator.

A subset of other useful tools (and reference material):

BLOCKS (compare against a database of sequence "blocks")
GeneMark.hmm gene prediction (has been "trained" with P. aeruginosa datasets)
NCBI-BLAST (search against NCBI's nr database or organism-specific databases)
NCBI-Compare against COGs database (Clusters of Orthologous Groups)
NCBI-Entrez (retrieve sequences from databases)
PSORT - Predicts protein localization within cells (warning: there are limitations to this analysis)
SignalP: signal sequence prediction and cleavage
ExPASy - Protein Molecular Weight and pI determination
EMBL - PredictProtein server (secondary structure prediction/topology)
Lipper Center for Computational Genetics
"The Bacterial Code" (NCBI's translation table 11 and notes)
ENZYME - ExPASy's enzyme nomenclature database (with nice pathway links that utilize Boehringer Mannheim's "Biochemical Pathways" map)
EcoCycE. coli genes and metabolism.
ChemFinder (another good chemical database with links)
Transporters in Prokaryotes (genomic comparison of transporters in prokaryotes by Ian Paulsen)
ExPASy Proteomics Tools (more tools/analyses)
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