Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
Photo
- - - - -

Sequence alignment with respect to a motif


  • Please log in to reply
4 replies to this topic

#1 noelmathur

noelmathur

    Enthusiast

  • Active Members
  • PipPipPipPipPip
  • 72 posts
1
Neutral

Posted 16 March 2009 - 01:57 AM

Hello All,

I am interested in the nearby region (500 bp either side) of a transcription factor binding motif. I know the genes that transcription factor binds to. I would like to take that 1kb region and align with respect to the transcription factor binding motif i.e. the motif remains at the centre and then the rest of the alignment should take place.

Does anybody know any program that can do this?

Thanks in advance.

#2 T C

T C

    Veteran

  • Active Members
  • PipPipPipPipPipPipPipPipPipPip
  • 277 posts
0
Neutral

Posted 16 March 2009 - 05:36 AM

Hey

Not an expert at this but this is what I think:

You should take all yr sequences together and do a multiple sequencing alignment. This should align yr motif in all sequences and also align the flanking sequences. However, if this doesn't work, you can take the sequences N-terminus of yr motif and align them, then do the same for sequences whcih are C terminus. Now you have alignment across the motif.

Take it with a word of caution, i am not sure if this is the right way to go about it. But its an idea for sure :)

Hope it helps

Best
TC

#3 noelmathur

noelmathur

    Enthusiast

  • Active Members
  • PipPipPipPipPip
  • 72 posts
1
Neutral

Posted 16 March 2009 - 10:47 PM

Thanks TC,
I did think in the same way but I wasn't too sure either so thought of putting this question to the fellow folks.

If anyone has any other idea or know how to do it, pleas drop the line.

#4 Springbok

Springbok

    member

  • Members
  • Pip
  • 5 posts
0
Neutral

Posted 24 May 2009 - 12:18 AM

You should do a multiple sequence alignment and then manually edit the alignment to check that it has been done to match your specific interests, i.e. that the transcription factor binding motif is aligned the way you want it. All of this can be done using Geneious www.geneious.com

#5 phage434

phage434

    Veteran

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 2,484 posts
251
Excellent

Posted 24 May 2009 - 08:24 AM

RSA Tools, http://rsat.ulb.ac.b...attern_form.cgi
has a feature somewhat similar to this which might be useful to you.




Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.