trimseq.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>[-sequence]<br>(Parameter 1)</td>
<td>(Gapped) sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
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<tr>
<td>[-outseq]<br>(Parameter 2)</td>
<td>Sequence set(s) filename and optional format (output USA)</td>
<td>Writeable sequence(s)</td>
<td><i>&lt;*&gt;</i>.<i>format</i></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>-window</td>
<td>This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage.</td>
<td>Any integer value</td>
<td>1</td>
</tr>

<tr>
<td>-percent</td>
<td>This is the threshold of the percentage ambiguity in the window required in order to trim a sequence.</td>
<td>Any numeric value</td>
<td>100.0</td>
</tr>

<tr>
<td>-strict</td>
<td>In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
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<tr>
<td>-star</td>
<td>In protein sequences, trim off not only X's, but also the *'s</td>
<td>Boolean value Yes/No</td>
<td>No</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>-[no]left</td>
<td>Trim at the start</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr>
<td>-[no]right</td>
<td>Trim at the end</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

</table>