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Pseudomonas syringae

Pseudomonas syringae pv. syringae is the cause of brown spot on bean and represents an important model in molecular plant pathology. Sequencing and annotation of the 6.09 megabase genome was completed by The Department of Energy Joint Genome Institute (DOE-JGI) in 5/05.

BLAST - link to P. s. syringae B728a BLAST page at NCBI
BLAST - link to P. s. syringae B728a BLAST page at DOE-JGI

This site allows users to search for various terms in one or more of the sequenced Pseudomonas genomes (plasmids excluded), with access to annotation records and GBrowse views.
P. syringae records in this database last updated: 8-05

Psy B728a complete genome - home pages for the B728a genome at NCBI  > and DOE-JGI  >
Genome annotation > - link to various analyses of the P. s. syringae B728a genome by the Computational Biology Program at ORNL

1. Go to the Artemis Release 8 > page at Sanger and click on Launch Artemis. Select the "Open with JNLPFile (default)" option. The Artemis Launch window will appear.

2. Go to "File>Open EBI Dbfetch" in the Artemis Launch window menu. When prompted, enter the accession number of the entry you wish to view.

Update frequency: Recent annotation updates are usually reflected in the following databases within a month of their posting on the PPI updates page (see updates >). However, users are advised that the EMBL/EBI/Genbank versions tend to be updated more rapidly than RefSeq.

3. Artemis can display multiple feature files superimposed on the main entry. View sample Artemis display with feature files >. The table below contains a list of files corresponding to a virulence-related features.

To view these in Artemis, open the desired file by clicking on the file name. Save to your hard drive with a .tab or .txt extension. Open the file from the menu of the main Artemis window using "File>Read an Entry..." (prior loading of the sequence file is required, as the tab files do not contain any DNA sequence).

Feature files for the Psy B728a chromosome

For users interested in downloading the Artemis program and genome files, or wanting more detailed descriptions of Artemis capabilities, detailed instructions can be found at the following links:

Artemis tutorial for PPI users  >
Artemis manual from the Sanger Institute  >
Artemis FAQ for PPI users  >

Contact the PPI project coordinator if you have further questions, or if you have a list of genes or other features for which you would like to have a formatted feature file >

The Artemis Comparison Tool (ACT) > is a DNA sequence comparison viewer developed at the Sanger Institute > and based on Artemis. Like Artemis, ACT can read sequences in Genbank or EMBL format, and display annotation and feature files of interest. Use of ACT is greatly eased by the option to launch the program over the network, and more recently, the capability to generate blastn and tblastx genome comparison files using WebACT  >, a utility developed at Imperial College, London  > to supplement ACT capabilities.

Compare genomes:

OPTION 1: Use the precomputed comparisons at WebACT
(sequence/annotations current as of: 1/1/06)

1. Go to WebACT Pre-Computed >>

2. Select the genomes you wish to align
(list now includes Pst DC3000, Psy B728a, and Psp 1448A in addition to P. aeruginosa, P. fluorescens, and P. putida).

3. Follow the prompts on the site until you get to Start ACT which allows the user to web launch the ACT and view the comparisons.

OPTION 2: Generate de novo comparisons using WebACT

WebACT can generate blastn or tblastx comparison files from either sequence/annotation files uploaded from your hard drive or RefSeq accession numbers. The advantage to using this approach is that the sequences downloaded from NCBI will reflect the most recent updates to the annotation.

RefSeq accession numbers for all P. syringae genome files are listed below. NOTE: if you are asked for a password on attempting to access files on the NCBI FTP site, hit 'cancel' and try again.

Update frequency: Recent annotation updates are usually reflected in the following databases within a month of their posting on the PPI updates page (see updates >). However, users are advised that the EMBL/EBI/Genbank versions tend to be updated more rapidly than RefSeq.

Sequence/Entry	EMBL/EBI/Genbank accession	RefSeq accession
Pst DC3000 chromosome	AE016853	NC_004578
Pst DC3000 pDC3000A	AE016855	NC_004633
Pst DC3000 pDC3000B	AE016854	NC_004632
Psy B728a chromosome	CP000075	NC_007005
Psp 1448A chromosome	CP000058	NC_005773
Psp 1448A p1448A-A	CP000059	NC_007274
Psp 1448A p1448A-B	CP000060	NC_007275

1. Go to the WebACT Generate > site. Upload sequence/annotation files from your hard drive or paste in the RefSeq accession number (shown in the table above). Generate the comparison file as instructed.

2. Upon completion of the comparison, WebACT gives the option to download files or start ACT. Launching ACT from the WebACT site is the fastest means of viewing comparison results, but if you wish to save the comparison files beyond the 7 days for which they are accessible on the WebACT server, they can be downloaded and subsequently viewed by launching ACT from the Sanger ACT site >.

3. Feature/TAB files specifying gene classes of interest can be superimposed on the sequence and annotation in the ACT display. For details, see instructions in the Artemis section of Tools for Genome Analysis >

For more information, visit the Pseudomonas syringae Genome Resources Home Page >>