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Is is possible that motifmatchr support the Minimal MEME Motif Format #6

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shangguandong1996 opened this issue Sep 28, 2019 · 0 comments

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@shangguandong1996
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when using the motifMatches() to scan the sequence in chromVAR , I awalys use JASPAR2016/JASPAR2018 to get the PFMatrix. But the number of motif in database is limited. And some motif I interested in is not in database. I am wondering whether I can use the MEME suite result like this
`
MEME version 4.4

ALPHABET= ACGT

strands: + -

Background letter frequencies (from file `../../promoter_background/Ath.bg'):
A 0.33230 C 0.16770 G 0.16770 T 0.33230

MOTIF AT1G01060 MP00119

letter-probability matrix: alength= 4 w= 10 nsites= 599 E= 4.8e-803
0.854758 0.001669 0.051753 0.091820
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.996661 0.003339 0.000000 0.000000
0.000000 0.013356 0.008347 0.978297
0.005008 0.000000 0.005008 0.989983
0.085142 0.010017 0.000000 0.904841
0.287145 0.076795 0.056761 0.579299
0.188648 0.240401 0.195326 0.375626

URL http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=AT1G01060.1#bind_motif

`

If it support, the number of motif scaning the sequence is no longer restricted when I use ChromVAR to computeDeviations :)

Best Regard

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