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
