Question: Using Meme PWM in HOMER for searching occurance of a motif in a set of sequences
0
gravatar for bdk
2.9 years ago by
bdk0
bdk0 wrote:

Hi All, i want to search following PWM using HOMER in a set of sequences. I actually created this for FIMO .

MEME version 4

ALPHABET= ACGT

strands: + -

Background letter frequencies (from uniform background): A 0.25000 C 0.25000 G 0.25000 T 0.25000

MOTIF hox-pbx_bipartite WRATNNATKR

letter-probability matrix: alength= 4 w= 10 nsites= 10 E= 0 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.250000 0.250000 0.250000 0.250000 0.250000 0.250000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.500000 0.000000 0.500000 0.000000

when i am using this file to search using HOMER , i am getting error that motif file is not found. It means that this PWM needs change is format or some other information is also needs to be included. How to use a motif in meme format in HOMER. do any conversion tool is available. Thanks

motif search chip-seq homer • 1.3k views
ADD COMMENTlink written 2.9 years ago by bdk0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2454 users visited in the last hour