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Revision 1.4 - (download) (annotate)
Mon Sep 9 21:21:20 2013 UTC (6 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2014_0729
Changes since 1.3: +8 -3 lines
Add pointer to myRAST for batch upload; remove words about phages/frags.

<h1> Upload a Genome</h1>

[% IF errors == '' %]

<p>A prokaryotic genome in one or more contigs should be uploaded in
either a single <a target=_blank
href='http://en.wikipedia.org/wiki/Fasta_format'>FASTA</a> format file
or in a Genbank format file. Our pipeline will use the taxonomy
identifier as a handle for the genome. Therefore if at all possible
please input the numeric <ahref='http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi'>taxonomy
identifier</a> and genus, species and strain in the following upload
workflow.</p>

<p>Please note, that only if you submit all relevant contigs (i.e. all
chromosomes, if more then one, and all plasmids) that comprise the
genomic information of your organism of interest in one job, Features
like <em>Metabolic Reconstruction</em> and <em>Scenarios</em> will
give you a coherent picture.</p>

<p>If you wish to upload multiple genomes at once, you may be interested
in using the batch upload interface that is available in the 
<a href="http://blog.theseed.org/servers/installation/distribution-of-the-seed-server-packages.html">myRAST distribution.</a>
See <a href="http://blog.theseed.org/servers/usage/the-rast-batch-interface.html">this
tutorial</a> for more information on this capability.</p>

<p><strong>Confidentiality information:</strong> Data entered into the
server will not be used for any purposes or in fact integrated into
the main SEED environment, it will remain on this server for 120 days
or until deleted by the submitting user. </p>

<p><strong>If you use the results of this annotation in your work,
please cite:</strong><br/><em>The RAST Server: Rapid Annotations using
Subsystems Technology.</em><br/>Aziz RK, Bartels D, Best AA, DeJongh
M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer
F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D,
Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O,
Vonstein V, Wilke A, Zagnitko O.<br/><em>BMC Genomics, 2008, [ <a
href="http://www.ncbi.nlm.nih.gov/pubmed/18261238"
target="_blank">article</a> ]</em></p>

<p><strong>File formats:</strong> You can either use <a target=_blank
href='http://en.wikipedia.org/wiki/Fasta_format'>FASTA</a> or Genbank
format. </p>

<ul><li>If in doubt about FASTA, <a target=_blank href='http://thr.cit.nih.gov/molbio/readseq/'>this service</a> 
allows conversion into FASTA format.</li>

<li>Due to limits on identifier sizes imposed by some of the 
third-party bioinformatics tools that RAST uses, we limit
the size of contig identifiers to 70 characters or fewer.</li>

<li>If you use Genbank, you have the option of preserving the gene
calls in the options block below. By default, genes will be
recalled.</li>
</ul>

<p><strong>Please note:</strong> This service is
intended for complete or nearly complete prokaryotic genomes, phages,
or plasmids.</p>

[% ELSE %]
<h2>Upload Error</h2>

There was an error with your genome upload:
<p>
[% errors %]
</p>
[% END %]

[% form.start %]
<fieldset> 
<legend>File Upload:</legend>
<table>
<tr><td>Sequences File</td>

<td>[% form.field.sequences_file.field %] </td>
</tr>
</table>
</fieldset>
<p>
[% form.submit %]
[% form.end %]

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