PPI logo P. s. pv. tomato DC3000 P. s. pv. phaseolicola 1448A
Genome Comparison with ACT

genome resources
home page

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.

- Psp 1448A genome

- 1448A/DC3000 comparison

- Pto DC3000 genome

- DC3000/B728a comparison

- Psy B728a genome

Fig C - Pairwise blastn comparisons between the Pto 1448A and Pto DC3000 genomes and between the Pto DC3000 and Psy B728a genomes displayed using the Artemis Comparison Tool (ACT)

Compare genomes using ACT

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 Pto 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 your own comparisons using WebACT

1. Download sequences for comparison from the NCBI FTP site.

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

Pto DC3000 chromosome NC_004578
Pto DC3000 pDC3000A NC_004633
Pto DC3000 pDC3000B NC_004632
Psy B728a chromosome NC_007005
Psp 1448A chromosome NC_005773
Psp 1448A p1448A-A NC_007274
Psp 1448A p1448A-B NC_007275

2. Go to the WebACT Generate site. Upload sequence/annotation files or paste in the RefSeq accession number (shown in the table above). Generate the comparison file as instructed.

3. 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.

4. 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



Magdalen Lindeberg
PPI Project Coordinator
Dept Plant Pathology
Cornell University