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1 : olson 1.1 <h1> Upload a Genome</h1>
2 :    
3 :     <p>A prokaryotic genome in one or more contigs should be uploaded in
4 :     either a single <a target=_blank
5 :     href='http://en.wikipedia.org/wiki/Fasta_format'>FASTA</a> format file
6 :     or in a Genbank format file. Our pipeline will use the taxonomy
7 :     identifier as a handle for the genome. Therefore if at all possible
8 :     please input the numeric <ahref='http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi'>taxonomy
9 :     identifier</a> and genus, species and strain in the following upload
10 :     workflow.</p>
11 :    
12 :     <p>Please note, that only if you submit all relevant contigs (i.e. all
13 :     chromosomes, if more then one, and all plasmids) that comprise the
14 :     genomic information of your organism of interest in one job, Features
15 :     like <em>Metabolic Reconstruction</em> and <em>Scenarios</em> will
16 :     give you a coherent picture.</p>
17 :    
18 :     <p><strong>Confidentiality information:</strong> Data entered into the
19 :     server will not be used for any purposes or in fact integrated into
20 :     the main SEED environment, it will remain on this server for 120 days
21 :     or until deleted by the submitting user. </p>
22 :    
23 :     <p><strong>If you use the results of this annotation in your work,
24 :     please cite:</strong><br/><em>The RAST Server: Rapid Annotations using
25 :     Subsystems Technology.</em><br/>Aziz RK, Bartels D, Best AA, DeJongh
26 :     M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer
27 :     F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D,
28 :     Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O,
29 :     Vonstein V, Wilke A, Zagnitko O.<br/><em>BMC Genomics, 2008, [ <a
30 :     href="http://www.ncbi.nlm.nih.gov/pubmed/18261238"
31 :     target="_blank">article</a> ]</em></p>
32 :    
33 :     <p><strong>File formats:</strong> You can either use <a target=_blank
34 :     href='http://en.wikipedia.org/wiki/Fasta_format'>FASTA</a> or Genbank
35 :     format. </p>
36 :    
37 :     <ul><li>If in doubt about FASTA, <a target=_blank href='http://thr.cit.nih.gov/molbio/readseq/'>this service</a>
38 :     allows conversion into FASTA format.</li>
39 :    
40 :     <li>If you use Genbank, you have the option of preserving the gene
41 :     calls in the options block below. By default, genes will be
42 :     recalled.</li>
43 :     </ul>
44 :    
45 :     <p><strong>Please note:</strong> This service is
46 :     intended for complete or nearly complete prokaryotic genomes. For now
47 :     we are not able to reliably process sequence data of very small size,
48 :     like small plasmid, phages or fragments.</p>
49 :    
50 :     [% IF errors != '' %]
51 :     There was an error with your genome upload:
52 :     <pre>
53 :     [% errors %]
54 :     </pre>
55 :     [% END %]
56 :    
57 :     [% form.start %]
58 :     <fieldset>
59 :     <legend>File Upload:</legend>
60 :     <table>
61 :     <tr><td>Sequences File</td>
62 :    
63 :     <td>[% form.field.sequences_file.field %] </td>
64 :     </tr>
65 :     </table>
66 :     </fieldset>
67 :     <p>
68 :     [% form.submit %]
69 :     [% form.end %]

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