119 lines
4.4 KiB
HTML
119 lines
4.4 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<html>
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<head>
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<title>BankIt Submission Help: Organism Table</title>
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<h1>Providing Organism for Multiple Sequences</h1>
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<div class="border1"><p>If you have not included organism names in your
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nucleotide FASTA definition lines, BankIt can accept organism names for
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multiple sequences in two ways: as a <strong>tab-delimited</strong> text
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file (as described below) or by applying the same organism to all sequences
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in the set using the web input form.
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</p>
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<p>To apply the same organism name (for example, in a population set) input
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the name in the 'Name' field on the 'Organism and Source Modifiers' page. A
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prompt in that field will display our most common organism names based on
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your input; this is NOT an exhaustive list. Unique descriptive information
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(such as strains, isolates, clones, or specimen vouchers) can then be
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provided in a Source Modifier table.
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</p>
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<p>To provide different organism names, a two-column, tab-delimited table
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containing the Sequence_ID and organism name for every sequence in the
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submission is used.</p>
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</div>
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<h2>Contents of the Organism Table</h2>
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<div class="border1"><p>The first row in the table contains the headers for
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each column: Sequence_ID and Organism, which must be verbatim, as in the
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example table below.</p>
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<p>The first column contains the Sequence_IDs used to identify each sequence in the <a href="fasta.html">nucleotide FASTA file</a>.</p>
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<p>The second column contains the name of the organism from which the
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corresponding sequence was isolated.</p>
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<p>Each sequence in the set must have a line in the Organism table. </p>
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<p>Each Sequence_ID may appear only once in the Organism table.</p>
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<table class="example">
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<caption>Sample Organism Table</caption>
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<tr>
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<td nowrap> Sequence_ID </td>
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<td nowrap> Organism </td>
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</tr>
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<tr>
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<td nowrap> Seq1 </td>
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<td nowrap> Carpodacus mexicanus </td>
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</tr>
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<tr>
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<td nowrap> Seq2 </td>
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<td nowrap> Uncultured Bacillus sp. </td>
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</tr>
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<tr>
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<td nowrap> Seq3 </td>
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<td nowrap> Phalaenopsis equestris var. leucaspis</td>
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</tr>
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<tr>
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<td nowrap> Seq4 </td>
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<td nowrap> Uncultured Archaeon </td>
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</tr>
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<tr>
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<td nowrap> Seq5 </td>
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<td nowrap> Influenza A virus </td>
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</tr>
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<tr>
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<td nowrap> Seq6 </td>
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<td nowrap> Vireo gilvus </td>
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</tr>
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<tr>
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<td nowrap> Seq7 </td>
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<td nowrap> Pelecanus erythrorhynchos </td>
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</tr>
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<tr>
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<td nowrap> Seq8 </td>
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<td nowrap> Hippodamia tredecimpunctata tibialis</td>
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</tr>
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<tr>
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<td nowrap> Seq9 </td>
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<td nowrap> Petunia integrifolia subsp. inflata</td>
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</tr>
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<tr>
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<td nowrap> Seq10 </td>
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<td nowrap> Fusarium oxysporum f. tuberosi</td>
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</tr>
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<tr>
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<td nowrap> Seq11 </td>
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<td nowrap> Dendroica tigrina </td>
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</tr>
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</table>
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<p><a href="sample_files/org-table-sample.txt">Sample Organism Table</a> (right-click to save) as a <strong>tab-delimited</strong> text file.</p>
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</div>
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<h2>Saving the Organism Table</h2>
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<div class="border1"><p>When using a spreadsheet program, be sure to save your file as <strong>tab-delimited</strong> text. If you are not sure that the "Save" option in your program will do this for you, use "Save As..."</p>
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<p>In Excel, select "Save As..." from the File menu. In the "Save as type:" pull-down menu, select "Text (Tab delimited) (*.txt)."</p>
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</div>
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</body>
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