How do I perform a motif search on a specific fasta sequence?

Question

[a.rex]

I have an annotated genome file, and I have a potential ncRNA that could be an eRNA.

I have extracted this sequence to a fasta file, and want to use homer for scanning transcription factor binding sites (i.e. to work out whether it is a potential enhancer).

How can I do this? I have tried with this command but it comes up with the error:

 perl findMotifs.pl input.fa fasta motifResults/ -fasta genome.fa 

Scanning input files... !!! Something is wrong... are you sure you
chose the right length for motif finding? !!! i.e. also check your
sequence file!!!

Scanning input files... !!! Something is wrong... are you sure you
chose the right length for motif finding? !!! i.e. also check your
sequence file!!!

[steve]

If you already have the fasta file then I would just use MEME-ChIP; http://meme-suite.org/tools/meme-chip

[lieven.sterck]

Can you post an extract of the fasta file(s) you're using?