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| View genomes in Artemis via remote launch (for high speed connections) |
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view
sample Artemis display
- Go to the Artemis page at Sanger
Click on the Download tab that appears there
Under Java Web Start click on:
Select the "Open
with Java Webstart Launcher" option. The Artemis launch window will appear.
- Go to "File>Open EBI Dbfetch" in the Artemis launch window menu.
When prompted, enter the EBI accession number (see the table below) 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, the EMBL/EBI/Genbank databases reflect updates more rapidly than RefSeq.
- Artemis can display multiple feature files superimposed on the main entry. View feature files available for the P. syringae genomes
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| View genomes in Artemis via downloaded program and sequence files |
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In some cases it is preferable to download the Artemis program rather than launching it remotely. To download, go to the Artemis page at Sanger, select the Download tab, and follow the instructions appropriate for your operating system.
Sequence files can be downloaded from the FTP site at NCBI or EMBL (accessible by the hyperlinked accession numbers in the table above). For more detailed information on running Artemis from your local system, go to the following resources:
Artemis
tutorial for PPI users
Artemis
manual from the Sanger Institute
Artemis FAQ
for PPI users
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| Viewing specific genome features in Artemis: |
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Artemis can display multiple feature files superimposed on the main entry. To download the feature files listed, open by clicking on the file name and save as text. Artemis can read files with various extensions including .txt. .tab and .gff. View
sample Artemis display with feature files.
Feature
files for the Pto DC3000 chromosome
(unless otherwise specified, these files were last updated 4-17-06)
| File
name |
features
included |
display
color in Artemis |
Variable Regions
(last loaded 7-14-08) |
Variable Regions (described in Lindeberg et al, 2008) |
[yellow] |
| TTSS
and substrates.txt |
genes
and protein products (CDS) for the Type III secretion system components |
[brown] |
| confirmed
and candidate effectors |
[red] |
hrp boxes.txt
(last loaded 1-3-07)
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experimentally
confirmed hrp boxes |
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| siderophores.txt |
genes
and protein products (CDS) implicated in siderophore biosynthesis |
[orange] |
| diffusible
toxins.txt |
genes
and protein products (CDS) implicated in coronatine biosynthesis |
[blue] |
| encoding
predicted non-ribosomal peptide synthetases (NRPS) |
[light
blue] |
| CW
vir factors.txt |
genes
and protein products (CDS) involved in synthesis of cell-wall associated virulence
factors |
[green] |
| flagella |
[pale green] |
mobile.txt
(last loaded 1-4-07)
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genes
and protein products (CDS) for mobile genetic elements |
[purple] |
| ipx
hits.txt |
genes
and protein products (CDS) induced during infection of Arabidopsis (Boch et al.
2002. Mol. Microbiol. 44:73) |
[yellow] |
| unique
unknowns.txt |
hypothetical
genes of unknown function not present in P. aeruginosa or P. putida,
(see supporting Table 6 of Buell,
et al. 2003 ) |
[magenta] |
| LSR.txt |
lineage
specific regions based upon comparison of of the DC30000 genome with P. aeruginosa and P. putida. (See Joardar, et al. 2005 and supplementary Table S3.) |
[pale
green] |
Feature
files for Pto DC3000 plasmids pDC3000A and pDC3000B:
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| Feature
files for the Psp 1448A chromosome |
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TTSS
and substrates.txt
(last loaded 1-3-07) |
genes
and protein products (CDS) for the Type III secretion system components |
[brown] |
| confirmed
and candidate effectors |
[red] |
hrp-boxes.txt
(last loaded 1-3-07) |
hrp promoter sequences described in Vencato et al, 2006 |
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| siderophores
and NRPS.txt |
genes
and protein products (CDS) implicated in biosynthesis non-ribosomal peptide synthetases
(NRPS) including the siderophores: achromobactin, yersiniabactin, and pyoverdin |
[light
blue] |
| CW
vir factors.txt |
genes
and protein products (CDS) involved in synthesis of cell-wall associated virulence
factors |
[green] |
| flagella.txt |
genes
and protein products (CDS) for flagellar components |
[pale green] |
| mobile.txt |
genes
and protein products (CDS) for mobile genetic elements |
[purple] |
Feature
files for Psp 1448A plasmid p1448A-A:
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| Feature
files for the Psy B728a chromosome |
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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
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| Align and view genomes with the Artemis Comparison Tool (ACT) |
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view sample ACT display
- To view pre-computed genome comparisons go to WebACT Pre-Computed
(versions of the genomes used in the pre-computed comparisons are only current as of 1/1/06)
- To generate de novo genome comparisons go to WebACT Generate
(input the Genbank accession numbers in the table to generate comparisons with the most up-to-date annotation)
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The Pseudomonas Genome Database allows users to search annotation records, and view in GBrowse one or more of the sequenced Pseudomonas genomes (plasmids excluded). P. syringae records in this database last updated: 9/05
view sample GBrowse window
view sample locus page
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