How to search with a motif matrix against my own sequences?

Question

[RNAseq]

I have a list of sequences from open DNA regions and I want to find from a predefined list of motifs which of these motifs have the highest scores in the open DNA regions. I have the motifs in Matrix format from the JASPAR database:

>MA0001.1 AGL3
      A  [ 0  3 79 40 66 48 65 11 65  0 ]
      C  [94 75  4  3  1  2  5  2  3  3 ]
      G  [ 1  0  3  4  1  0  5  3 28 88 ]
      T  [ 2 19 11 50 29 47 22 81  1  6 ]

and a list of sequence locations in BED files (which I can convert to fasta sequences). Is there a program where I can give a list of motif matrices + bed files or fasta sequences, and get a list of scores per motif for each sequence?

Answer 1

[dago]

You can use the nice RSAT suit with the function "matrix scan" OR you can use the MEME suit if it is not a TF binding site

Answer 2

[Santosh Anand]

You can use FIMO from the MEME suite. Here is the Manual. The motifs need to be in meme format. Look for the program jaspar2meme on their web which does the conversion. Alternatively, you can also use their pre-compiled JASPAR motifs in meme format