How Can I Convert Yetfasco Matrix To A Jaspar/Transfac One?

Question

[pollyD]

I perform an analysis of overrepresented transcription factor binding sites using oPOSSUM.

The issue is the following: I need to use some profiles that are not included in JASPAR. I can get those from YeTFaSCo. Then I need to convert those to JASPAR format to run oPOSSUM analysis. As far as I understand, both databases (YeTFaSCo and JASPAR) claim that they contain PFMs. But the same logos are associated with different matrices (for example, this and this represent the same motif).

Is it possible to convert a matrix from YeTFaSCo to JASPAR format?

I would appreciate any help. Thanks in advance!

Answer 1

[Tky]

You may use the convert matrix in RSA tool set, check the left panel under matrix tools.

Just drop the matrix copied form YeTFFaSCo as tab format and select the output format as JASPAR, and then it is done.

For example, you target matrix looks like this in JASPAR format
>convert-matrix_2013-06-11.091446_ONQTGz_input.tab_1 convert-matrix_2013-06-11.091446_ONQTGz_input.tab_1
A  [0.181387 0.386457 0.002036 0.121673 0.0 0.001221 0.17284 ]
C  [0.184759 0.091376 0.977795 0.0 0.851711 0.001506 0.182402 ]
G  [0.304358 0.172992 0.017835 0.878327 0.0 0.995872 0.095864 ]
T  [0.329496 0.349175 0.002335 0.0 0.148289 0.001401 0.548894 ]

[pollyD]

Thanks a lot! I've tried this tool before but was not sure about the input format.

[pollyD]

Now I know two mistakes I made. They are pretty silly. First, the JASPAR database rounds to two digits, and I this makes the the same matrix different for the program. Second, some matrices may be reverse complement. Thanks a lot again!

[Tky]

It is great to hear that, and thanks for sharing the your experience :-)