How To Convert A Transfac Pssm Into Meme Format?

Question

[Anima Mundi]

Hello,

I would like to convert automatically a PSSM from TRANSFAC to MEME format.

Here there is an example of a set of lines related to a matrix:

MEME version 4.0

ALPHABET= ACGT

strands: + -

Background letter frequencies (from dataset without add-one prior applied): A 0.276 C 0.224 G 0.224 T 0.276

MOTIF 2

BL MOTIF 2 width=26 seqs=23 letter-probability matrix: alength= 4 w= 26 nsites= 23 E= 1

In particular, I do not know: a) how to deal with the "Background letter frequencies" lines (as I start from a TRANSFAC); b) how to deal with E value (just set it to 0?).

Answer 1

[James]

Hi Anima,

If you download a copy of the MEME distribution there is a script called transfac2meme which can convert the transfac matrix.dat file into the minimal MEME format. To get the databases we use on the official meme.nbcr.net site we use the command:

transfac2meme -use_acc -logodds \
    -url "https://portal.biobase-international.com/cgi-bin/build_t/idb/1.0/pageview.cgi?view=MatrixReport&matrix_acc=MOTIF_NAME" \
    ../TRANSFAC_2009.4/dat/matrix.dat > ! ../transfac_matrix.meme

Obviously your paths would differ and if you're not using csh then you wouldn't use the > ! syntax to indicate file redirection.

[Anima Mundi]

This helps, thanks.

[Diana]

Can it also convert Jaspar matrices to MEME format? thanks!

Answer 2

[Stew]

If you would rather do this online, RSAT has a convert-matrix tool, which can do this along with lots of other motif related tasks.

[Anima Mundi]

This is useful too, but I did not find a way to obtain a MEME from a TRANSFAC. Thanks anyway.

[Stew]

Yes, sorry. I see MEME is an input option but not an output option.