digest.itable

emboss的linux版本的源代码

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>[-seqall]<br>(Parameter 1)</td>
<td>Protein sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>-menu</td>
<td>Select number</td>
<td><table><tr><td>1</td> <td><i>(Trypsin)</i></td></tr><tr><td>2</td> <td><i>(Lys-C)</i></td></tr><tr><td>3</td> <td><i>(Arg-C)</i></td></tr><tr><td>4</td> <td><i>(Asp-N)</i></td></tr><tr><td>5</td> <td><i>(V8-bicarb)</i></td></tr><tr><td>6</td> <td><i>(V8-phosph)</i></td></tr><tr><td>7</td> <td><i>(Chymotrypsin)</i></td></tr><tr><td>8</td> <td><i>(CNBr)</i></td></tr></table></td>
<td>1</td>
</tr>

<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i>&lt;*&gt;</i>.digest</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td colspan=4>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-aadata</td>
<td>Molecular weight data for amino acids</td>
<td>Data file</td>
<td>Eamino.dat</td>
</tr>

<tr>
<td>-unfavoured</td>
<td>Trypsin will not normally cut after a K if it is followed by (e.g.) another K or a P. Specifying this shows those cuts. as well as the favoured ones.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
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<tr>
<td>-ragging</td>
<td>Allows semi-specific and non-specific digestion. This option is particularly useful for generating lists of peptide sequences for protein identification using mass-spectrometry.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-termini</td>
<td>Select number</td>
<td><table><tr><td>1</td> <td><i>(none)</i></td></tr><tr><td>2</td> <td><i>(nterm)</i></td></tr><tr><td>3</td> <td><i>(cterm)</i></td></tr><tr><td>4</td> <td><i>(nterm OR cterm)</i></td></tr></table></td>
<td>1</td>
</tr>

<tr>
<td>-overlap</td>
<td>Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-allpartials</td>
<td>As for overlap but fragments containing more than one potential cut site are included.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

</table>