Pseudomonas Genome Database - Tools

Tools

Alternate Annotation Views
GBrowse
GBrowse provides an alternate view to genome annotations by fetching a region of the genome specified by a user's search criteria and presents the specified landmarks to the user in a detailed view containing one or more horizontal tracks representing individual sequence features for that area. The user is free to zoom in and out according to the level of magnification/resolution desired. Landmarks on each track usually contain a link to detailed information on additional websites.

GBrowse
Metabolic Pathways
PseudoCyc View enzymatic reactions and biochemical pathways in Pseudomonas aeruginosa PAO1. PseudoCyc contains information on P. aeruginosa PAO1 genes and proteins along with 821 enzymatic reactions and 141 biochemical pathways involving 738 enzymes and 651 compounds.

PseudoCyc View
Whole Genome Alignments
Mauve Mauve is a genome alignment tool designed to efficiently construct and view multiple genome alignments in the presence of large-scale evolutionary events. The Mauve viewer displays genomes as horizontal tracks aligned by matching genome sections. Pre-computed alignments for Pseudomonas aeruginosa, fluorescens, putida and syringae are available for viewing.


Aaron C.E. Darling, Bob Mau, Frederick R. Blatter, and Nicole T. Perna. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research. 14(7):1394-1403.

Mauve View
WebACT WebACT provides a database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool (ACT) developed by the Sanger Institute.

Abbott JC, Aanensen DM, Bentley SD, 2007 (Pubmed)

WebACT website
Sequence-based Searches
BLAST Perform BLAST searches against nucleotide and protein sequence databaes from all genomes in this database. Results can be viewed using our interface that allows you to sort results and add annotations associated with each high-scoring pair to a clipboard for comparison.
BLAST search page
Search for DNA motifs
This search tool accepts an IUPAC-formatted variable length DNA sequence and converts it into a regular expression used to search the Pseudomonas genome sequences. Upon search completion, an online report or downloadable tab-delimited file is produced containing information on all regions the motif is found in.
DNA motif search page
Retrieve Sequence Data
(Protein and DNA)

1) Retrieve specific genomic DNA sequences from all genomes in the database using coordinates specified in your search criteria. User has option to view reverse complement of the sequence and/or its translation.

2) Request the DNA or protein sequence of an ORF by specifying its Locus ID.

Sequence retrieval page