[Bio-software] alignment of motifs with conserved sequences

T Joshi via bio-soft%40net.bio.net (by tejalonline from gmail.com)
Mon Jun 4 03:48:21 EST 2007

Hi All !
This is my first email to this mailing list, and it might be a naive
question since I am also new to this field.
Anyways, my goal is to find out whether the motifs predicted by MEME
(and other algorithms)  from 5' UTR sequences are conserved across
species. For this I have two sets of sequences:
1) 5' UTR sequences of homo sapiens (collected from BioMart) with
Ensembl Gene ID.
2) I have downloaded sequences from the conservation track of UCSC
extracted from 5' UTR (exon) region with the intersection with ensembl

I am applying motif discovery algorithms on the first set of
sequences. Later, I do a multiple alignment of these motifs with the
second set of sequences(conserved 5' UTR) using clustalw.

Is this approach a proper one? If yes, then how do I read the output
of clustalw, i.e. alignment score and the dendrograph to find best
motifs which are conserved?

Guidance, suggestions please.
T Joshi

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