[ssml] Accurate searches in nucleotide databases

[Georg Fuellen]

Hello,

I'm looking for a (profile-based) search method with which
I could look for matches to a noncoding region of approx.
150 basepairs; I've already got the region for about 10 species;
homology was established by proximity to a gene locus.

Discontiguous Mega-Blast is not sensitive enough.

I'd like to search the standard NCBI databases (at least
NR & EST, optimally GSS, HTGS, WSS as well).
Any hints? Could the problem be framed as a search for
a very long transcription factor binding site, using
the 10 sequences I have to construct the position weight matrix?
If so, where could I search?

I'm grateful for any help
Georg Fuellen