Insertion sequences and flanking regions - (Mar/15/2011 )

Hello,

I found some insertion elements in genome of bacteria and in next step I extended the flanking regions to be able to study the function of these mobile elements. Could you help me with some advise how to analyse the flanking sequences? I have sequence with homology to transposases regions and with some functional genes but I can hardly asses what Insertion sequences have done. I will be gratefull for any advise,
Martha

if you not sure what IS element you really have you can check the identity at this web page:
My link

an IS can either disrupt a gene and render it disfunctional, indicated by the fact the the left and right flanking region is associated with the same gene ...insert in front of a gene and in some cases enhance transcription of the said gene ...or lead to large deletions by recombination if the same IS is inserted in proximity.

So if you have sequenced the flanking region it should be easy to asses what happend. First of all you have to find out where your IS element starts and where it ends ... if you find an transposase adjacent this means you havn't reached the "bacterial" sequence and you are still "inside" the IS element.

Regards,
p

Martha on Tue Mar 15 13:47:41 2011 said:

pDNA, Thank you for you answer. I found two different insertion elements, and they have homology with direct insertion sequences from data base but the problem is that I have flanking region of them only from one side. Maybe it would be enough to assess their function? What could you advise me?
Martha

What organism we are talking about? ...is a whole genome sequence available?

if you have one the flanking region ...what does it say? ...does the flanking region start within the middle of a gene?

you can make something like 2 step genome walking to elucidate the other flanking side ...for details see this publication.
But you have to be aware that implementing this methode is somehow laborious!

Regards,
p

Martha on Wed Mar 16 13:01:02 2011 said: