maskfeat.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>Sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>[-outseq]<br>(Parameter 2)</td>
<td>Sequence filename and optional format (output USA)</td>
<td>Writeable sequence</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>-type</td>
<td>By default any feature in the feature table with a type starting 'repeat' is masked. You can set this to be any feature type you wish to mask.
See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot feature types.
The type may be wildcarded by using '*'.
If you wish to mask more than one type, separate their names with spaces or commas, eg:
*UTR repeat*</td>
<td>Any string is accepted</td>
<td>repeat*</td>
</tr>

<tr>
<td>-tolower</td>
<td>The region can be 'masked' by converting the sequence characters to lower-case, some non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the case change. You might like to ensure that the whole sequence is in upper-case before masking the specified regions to lower-case by using the '-supper' flag.</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-maskchar</td>
<td>Character to use when masking.
Default is 'X' for protein sequences, 'N' for nucleic sequences.
If the mask character is set to be the SPACE character or a null character, then the sequence is 'masked' by changing it to lower-case, just as with the '-lowercase' flag.</td>
<td>Any string up to 1 characters</td>
<td>'X' for protein, 'N' for nucleic</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 colspan=4>(none)</td>
</tr>

</table>