Question: How To Convert A Transfac Pssm Into Meme Format?
4
gravatar for Anima Mundi
10.0 years ago by
Anima Mundi2.8k
Italy
Anima Mundi2.8k wrote:

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?).

binding pssm meme transcription • 7.2k views
ADD COMMENTlink modified 9.9 years ago by Stew1.4k • written 10.0 years ago by Anima Mundi2.8k
8
gravatar for James
10.0 years ago by
James80
James80 wrote:

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.

ADD COMMENTlink modified 17 months ago by Ram32k • written 10.0 years ago by James80

This helps, thanks.

ADD REPLYlink written 10.0 years ago by Anima Mundi2.8k

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

ADD REPLYlink modified 17 months ago by Ram32k • written 6.8 years ago by Diana850
4
gravatar for Stew
10.0 years ago by
Stew1.4k
Cambridge
Stew1.4k wrote:

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.

ADD COMMENTlink written 10.0 years ago by Stew1.4k
1

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

ADD REPLYlink written 10.0 years ago by Anima Mundi2.8k
1

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

ADD REPLYlink written 10.0 years ago by Stew1.4k
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