...
| HTML |
|---|
<center>
<br>
<img src="/wiki/download/attachments/22056023/Tandem Repeats Finding.jpg"/>
<br>
</center> |
The dialog parameters:
Tandem presetPresent Settings — specify the tandem repeats parameters with predefined values by selecting the available preset:
| HTML |
|---|
<center>
<br>
<img src="/wiki/download/attachments/4227627/Tandem Repeats Finding_1.png"/>
<br>
</center> |
Min period, Max period — the minimum and maximum .
Algorithm — the algorithm parameter allows to select the search algorithm. The default and a fast one is optimized suffix array algorithm.
Min length of repeated sequence - the minimum acceptable repeat length measured in base symbols.
Max length of repeated sequence - the mzximum acceptable repeat length measured in base symbols.Region to process —
Min length of tandem repeat - the minimum tandem size sets the limit on the minimum acceptable length of the tandem, i.e. the minimum total repeats length of the searched tandem.
Min number of repeats - the minimum number of repeats of a searched tandem.
Show overlapped tandems - check if the plugin should search for the overlapped tandems, otherwise keep unchecked.
Search in - specify the region to search in the whole sequence, a custom region or the region of the current selection (if any).
The output settings can be found in the Output tab:
In the Save annotation(s) to group you group, you can set up a file to store annotations. It could be either an existing annotation table object, a new annotation table or auto-annotations table (if it is available).
In the Annotation parameters group you , you can specify the name of the group and the name of the annotation. If the group name is set to <auto> UGENE will <auto> UGENE will use the group name as the name for the group. You can use the ‘/’ characters in this field as a group name separator to create subgroups. If the annotation name is set to by type UGENE will UGENE will use the annotation type from the Annotation type: table as the name for the annotation. Also you Also, you can add a description in the corresponding text field.
| HTML |
|---|
<center>
<br>
<img src="/wiki/download/attachments/16122333/Tandem Repeats Finding_2.png"/>
<br>
</center> |
Additional search options can be found in the Advanced tab:
Algorithm — the algorithm parameter allows to select the search algorithm. The default and a fast one is optimized suffix array algorithm.
Minimum tandem size — the minimum tandem size sets the limit on minimum acceptable length of the tandem, i.e. the minimum total repeats length of the searched tandem.
Minimum repeat count — the minimum number of repeats of a searched tandem.
Show overlapped tandems — check if the plugin should search for the overlapped tandems, otherwise keep unchecked.
| Children Display | ||
|---|---|---|
|