How to extract flanking regions using SciRoKo3.4 ?

Question

[Bara'a]

Hi all :)

I'm using SciRoKo 3.4 application for SSR and flanking regions extraction ... I've read the tutorial that comprehensively explains how to extract SSR from a .fasta file , but it never came across on how to extract flanking regions !!

While exploring this application I found out that functionality ; but the screen ( windows form ) that does so is black and I can't figure out what options do I have ... it was like sensing the way in a dark corridor!!

BTW .. I have uninstalled and reinstalled the application several times and the problem persists ; which made me conclude that this problem has nothing to do with my machine performance I guess !!

Can anyone help me with this ; please ?

Thanks in advance

Answer 1

[Bara'a]

I'm not sure whether it's legal for someone to write the answer on his own question , but I managed to find the solution and I would like to share it with others .

It turned out after four months of trial and error working with this tool that the mysterious options were as follows :

1. The first radio button allows the user to choose the length (bp) of each flanking region on both sides of a SSR , in which the upper text box is for the left flanking and the lower text box is for the right one excluding -of course- the length of the SSR itself .
2. The second radio button allows the user to choose the length (bp) of the entire retrieved sequence of both flanking regions including the length of the SSR.

Hope that this could be beneficial for someone out there facing this same problem.