Suggestions of tools to study the 5'UTR region of genes

[Fred]

Hello,


I would like to analyze the 5' UTR region of several genes in order to
find interesting regulation sequences.
SInce it has been a while that I did not perform such a task, I would
like to know from people that I used to do it, what are the most
convenient software, webservers to use.

Thanks in advance,

Fred

[Steve Lianoglou]

Hi Fred,

I thought I sent this, but I haven't seen it posted ... anyway, here's
some info:

1) Here's some links regarding the Tompa et al review of motif
discovery tools:
http://bio.cs.washington.edu/assessment/

2) Here are links to some other tools:
http://arep.med.harvard.edu/labgc/amcguire/IBSS/algorithms-links.html

3) Review of principles behind motif discovery:
http://www.nature.com/nbt/journal/v24/n8/full/nbt0806-959.html

3) Google "motif discovery" will get you a mess load more ..

HTH,
-steve

[Steve Lianoglou]

http://bio.cs.washington.edu/assessment/
Has a link to the Tompa et al review paper "Assessing Computational
Tools for the Discovery of Transcription Factor Binding Sites" and
other stuff

Googling for "motif discovery" also comes up with mucho. Here's
another page with a list of some tools, like AlignACE, MEME, etc.
http://arep.med.harvard.edu/labgc/amcguire/IBSS/algorithms-links.html

This looks interesting, too:
http://fraenkel.mit.edu/webmotifs/mdprogs.html

HTH,
-steve

[123 Bioinformatics]

Hi Fred,

   I can give you some Ideas regarding this.

step 1:
      You can Download GBK files of the particular  Genomes / Genes .

step 2:
      From the GBK files you can get the UTR regions(sequences) of the genes.
      and convert it to fasta format. For this you may have to write a Perl Scripts of your own to do that.

step 3: 
    To find the motifs in those sequence you can use normal BLASTN (In case you expect bigger motifs). Do blast against each sequence against each...Means you can create a database of those seqs for BLAST. And do BLAST for all the sequences against database.
 
Otherwise you can load these sequence in "MEME" with stringent e-values.  In case if you are searching for KNOWN MOTIFS
you can use SeedTop (comes with BLAST package)


In case if you want to write your own Perl/python/SHELL Script for finding Patterns, you can use Manti Carlo methods to finalise the motifs (cluster) P value.

Hope its helpful...

if  you have any questions regarding this dont hesitat eto ask me.

All the best.

Jeevan

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