blast MEME motif against yeast genomic DNA

Question

[nibhelim]

Hi there!

I would like to blast a MEME motif (21bp with the % of each base in each position) against the yeast genome, to find how many of these motif are in the genome and where.

Is there a program that can easily do that??

Thank you for the help!!!!

Answer 1

[dago]

I guess you have a Position weight matrix. There are different tools that allow you to scan your genomes. Some of them are reported in these posts:

• how to get promoter regions from a genome
• transcription factor binding site prediction software/server

There is also RSAT web site that is really great!

Answer 2

[Giovanni M Dall'Olio]

Use FIMO from the MEME suite, selecting the yeast database as target sequence. You can find the yeast genome inside Ensembl Genomes, Genbank Fungii Genomes, and UCSC-other.

You can do the alignment from the online interface, or download the suite in local and do it in your local computer.