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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.
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Psp 1448A genome
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1448A/DC3000 comparison
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Pto DC3000 genome
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DC3000/B728a comparison
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Psy B728a genome
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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
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
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