Other Features
==============

Mapping Analysis
----------------

The mapping analysis will locate the found repeats into gene features (CDS, UTR, intron, exon). Before mapping, you should import gtf or gff annotation files.

Go to **Toolbar**, and then click |locate| to perform mapping analysis. After mapping, the repeats mapped in gene exon (pink), intron (green), CDS (purple), 3'UTR (blue), 5'UTR (yellow) will be marked as different colors in table.

	.. figure:: _static/annotcolor.png

Design Primer
-------------

Krait2 use `primer3 <https://primer3.org/>`_ to design primers. Before primer design, you can set corresponding parameters for primer3. The meaning of primer3 tags can be found in `primer3 manual <https://primer3.org/manual.html>`_.

	.. figure:: _static/primersetting.png
		:width: 500
		:align: center

First, you should select some repeats in table, and then click |primer| to design primers. If primer designed successfully, the primers will be displayed in Primer result table.

	.. figure:: _static/primerresults.png
		:align: center

The description of each column in primer result table:

.. list-table:: 
	:header-rows: 1
	:align: center

	* - Column
	  - Description
	* - ID
	  - unique identifier generated by Krait
	* - locus
	  - repeat identifier which is composed of repeat type, input file id and repeat id
	* - entry
	  - primer entry id, each locus may has multiple designed primers
	* - product size
	  - product size
	* - strand
	  - forward or reverse
	* - Tm
	  - melting temperatures for forward and reverse primers
	* - GC content
	  - GC content for forward and reverse primers
	* - 3' End stability
	  - 3' end stability for forward and reverse primers
	* - primer sequences
	  - primer sequences for forward and reverse primers

Click the row in primer table, you can view the primer sequence location in input sequence file. The sequences enclosed by the dotted boxes are the positions of the primers.

	.. figure:: _static/primerseq.png
		:align: center

Perform Statistics
------------------

After searching repeat, you can click |statistics| to perform statistics analysis. Then, you can view the short statistics report in statistics tab.

	.. figure:: _static/statsresults.png

Motif Standardization
^^^^^^^^^^^^^^^^^^^^^

Before statistics analysis, Krait2 will standardize the motif sequence and provide four standardization levels.

**Level 0**

no standardization will be performed

**Level 1**

Standardize similar motifs. For example, AGA can be viewed as AAG. AAG can represent AAG, AGA and GAA.

**Level 2**

Standardize reverse complementary motifs, including Level 1. For example, CAT is a reverse complementary motif of ATG. ATG can represent TGA, GAT, CAT, ATC and TCA

**Level 3**

Standardize complementary motifs, including Level 1 and Level 2. For example, TAC is a complementary motif of ATG. ATG can represent TGA,GAT, CAT, ATC, TCA, TAC, ACT and CTA

**Level 4**

Standardize reverse motifs, including Level 1, Level 2 and Level 3. For example, GTA is a reverse motif of ATG. ATG can represent TGA,GAT, CAT, ATC, TCA, TAC, ACT, CTA, GTA, TAG and AGT

You can go to **Tool** menu, click **Show motif standardization** to view the representative motifs.

	.. figure:: _static/motifstandard.png

Filter Tables
-------------

The repeats in current table can be filtered by setting different conditions according to each column. Go to **Toolbar** and click |filter| to open filter dialog.

	.. figure:: _static/filterdialog.png
		:width: 500
		:align: center

Click |plus| to add filter condition, click |minus| to remove current filter condition, click |clear| to clear all filter conditions, after setting filters, you can click |update| update table to do filter and update the rows in current table.


.. |locate| image:: _static/locating.svg
	:width: 20
.. |primer| image:: _static/primer.svg
	:width: 20
.. |statistics| image:: _static/statistics.svg
	:width: 20
.. |filter| image:: _static/filter.svg
	:width: 20
.. |plus| image:: _static/plus.svg
	:width: 20
.. |minus| image:: _static/minus.svg
	:width: 20
.. |clear| image:: _static/clear.svg
	:width: 20
.. |update| image:: _static/update.svg
	:width: 20