Search Transcription Factor Binding Sites Based On Matrices

Question

[S.Retina]

Hello,

I would to predict the Transcription Factor Binding Sites of ~20,000 genes upstream 1000bp sequences. And I want to do this search based on matrices got from JASPAR (Archive.zip file).

For example:

>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 ]
>MA0003.1 TFAP2A
A  [  0   0   0  22  19  55  53  19   9 ]
C  [  0 185 185  71  57  44  30  16  78 ]
G  [185   0   0  46  61  67  91 137  79 ]
T  [  0   0   0  46  48  19  11  13  19 ]
>MA0004.1 Arnt
A  [ 4 19  0  0  0  0 ]
C  [16  0 20  0  0  0 ]
G  [ 0  1  0 20  0 20 ]
T  [ 0  0  0  0 20  0 ]

Thank the information from this link: http://biostar.stackexchange.com/questions/6436/transcription-factor-binding-site-prediction

But I still do not have a suitable tool to scan the set of sequences, because I use the PC windows XP system.

So, can you recommend some tools for me? or the other methods to do this work?

Thanks!

[S.Retina]

I found Cluster-Buster a third generation program for finding clusters of pre-specified motifs in nucleotide sequences. But perhaps it cannot completely output what I want. It outputs the clusters of motifs.

Answer 1

[Pasta]

You could use RSAT, and more precisely PATSER This tools asks for your matrix and your DNA sequences

[S.Retina]

Thank you for your help! I found the RSA-tools - matrix-scan is the better version. And I am trying to find another tool with stand-alone version that could be performed in PC windows. ....