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1 : olson 1.1 <h1> Upload a Genome</h1>
2 :    
3 : olson 1.2 [% IF errors == '' %]
4 :    
5 : olson 1.1 <p>A prokaryotic genome in one or more contigs should be uploaded in
6 :     either a single <a target=_blank
7 :     href='http://en.wikipedia.org/wiki/Fasta_format'>FASTA</a> format file
8 :     or in a Genbank format file. Our pipeline will use the taxonomy
9 :     identifier as a handle for the genome. Therefore if at all possible
10 :     please input the numeric <ahref='http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi'>taxonomy
11 :     identifier</a> and genus, species and strain in the following upload
12 :     workflow.</p>
13 :    
14 :     <p>Please note, that only if you submit all relevant contigs (i.e. all
15 :     chromosomes, if more then one, and all plasmids) that comprise the
16 :     genomic information of your organism of interest in one job, Features
17 :     like <em>Metabolic Reconstruction</em> and <em>Scenarios</em> will
18 :     give you a coherent picture.</p>
19 :    
20 :     <p><strong>Confidentiality information:</strong> Data entered into the
21 :     server will not be used for any purposes or in fact integrated into
22 :     the main SEED environment, it will remain on this server for 120 days
23 :     or until deleted by the submitting user. </p>
24 :    
25 :     <p><strong>If you use the results of this annotation in your work,
26 :     please cite:</strong><br/><em>The RAST Server: Rapid Annotations using
27 :     Subsystems Technology.</em><br/>Aziz RK, Bartels D, Best AA, DeJongh
28 :     M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer
29 :     F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D,
30 :     Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O,
31 :     Vonstein V, Wilke A, Zagnitko O.<br/><em>BMC Genomics, 2008, [ <a
32 :     href="http://www.ncbi.nlm.nih.gov/pubmed/18261238"
33 :     target="_blank">article</a> ]</em></p>
34 :    
35 :     <p><strong>File formats:</strong> You can either use <a target=_blank
36 :     href='http://en.wikipedia.org/wiki/Fasta_format'>FASTA</a> or Genbank
37 :     format. </p>
38 :    
39 :     <ul><li>If in doubt about FASTA, <a target=_blank href='http://thr.cit.nih.gov/molbio/readseq/'>this service</a>
40 :     allows conversion into FASTA format.</li>
41 :    
42 :     <li>If you use Genbank, you have the option of preserving the gene
43 :     calls in the options block below. By default, genes will be
44 :     recalled.</li>
45 :     </ul>
46 :    
47 :     <p><strong>Please note:</strong> This service is
48 :     intended for complete or nearly complete prokaryotic genomes. For now
49 :     we are not able to reliably process sequence data of very small size,
50 :     like small plasmid, phages or fragments.</p>
51 :    
52 : olson 1.2 [% ELSE %]
53 :     <h2>Upload Error</h2>
54 :    
55 : olson 1.1 There was an error with your genome upload:
56 : olson 1.2 <p>
57 : olson 1.1 [% errors %]
58 : olson 1.2 </p>
59 : olson 1.1 [% END %]
60 :    
61 :     [% form.start %]
62 :     <fieldset>
63 :     <legend>File Upload:</legend>
64 :     <table>
65 :     <tr><td>Sequences File</td>
66 :    
67 :     <td>[% form.field.sequences_file.field %] </td>
68 :     </tr>
69 :     </table>
70 :     </fieldset>
71 :     <p>
72 :     [% form.submit %]
73 :     [% form.end %]

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