identifying which SNPs sit in TFBS (Yeast)

Question

i have a set of ~11k SNPs for Saccharomyces cerevisiae, baker's yeast and i would like to identify which ones of these sit in transcription factor binding sites and if they do information on the relevant TFBS.

i've scoured this site and the internet and i couldn't find a downloadable database that would give me locations of all known/verified TFBS for yeast. i've studied the YEASTRACT website thoroughly but didn't find such database to download information about TFBS for all the ORFs/genes in one go.

moreover, when i tried getting the information manually through YEASTRACT search on-line i found results confusing. for example: searching for TF for ORF "YOL166W-A" returns a list of 4 TFs. clicking on one of them, say Sok2p, takes you to another page which says, amongst other things, that the corresponding TFBS is "acMTGCAKg"... what does it mean? (i know the ACTG alphabet but what are the 'a', 'c', 'K' and 'g' symbols?) and what does this tell me about the actual location of the binding site? do i have to BLAST the whole genome to identify it? (shouldn't there be a database with this info for yeast already?) if so, how do i BLAST for symbols like 'K' and 'g'?

i have background in stats but currently work in genetics applications, hence extracting relevant bioinformatics data is very confusing for me on occasions. any help will be appreciated.

Answer 1

I agree it can be extremely confusing sometimes to find the right data.

Do you know RSAT (Regulatory Sequences Analysis Toolkit) ? If you go in "help & contact", and "motif databases", you'll find the Yeastract database: http://rsat-tagc.univ-mrs.fr/rsat/motif_databases/Yeastract/

I thought it would also be on JASPAR, but couldn't find it.

Then for your analysis where you look for SNPs in the motifs, there is a tool on RSAT, that unfortunately works only with the Metazoa database right now, but you might be interested to check it out, and the corresponding paper: http://rsat-tagc.univ-mrs.fr/rsat/variation-scan_form.cgi

Answer 2

In addition to the 4 nucleotide letters, there are letters that mean "the letter is one of these two or three:

M = aMine = A or C

R = puRine = A or G

W = Weak (two hydrogen bonds) = A or T

S = Strong (three hydrogen bonds) C or G

Y = pYrimadine = C or T

K = Ketone = G or T

B = not A

D = not C

H = not G

U = not T

I would guess the the lowercase means that those letters are not as important as the uppercase ones in terms of determining binding.