Hi,
I am trying to use FIMO command line version with motifs inferred from short protein sequences (with length of 6-14) to scan short peptides.
As a test, I've used FIMO to scan the peptides dataset contributing to the inferred motifs. I observed that peptides shorter than 10 amino-acids were never discovered.
I've tried to change the e-value threshold in order to increase the number of hits, but still shorter peptides were not discovered.
In addition, I see cases where the correct motif was not associated with the correct sequence (i.e. sequence contributing to motif X is not a hit of motif X). The score and e-value of such hits were indeed much lower, however, still, the sequence was not associated with it true motif.
Therefore I have the following questions:
1. Is there some limitation in FIMO for hit length?
2. Do you have any advice how I can better use FIMO for my dataset (short protein sequences and short motifs).
Thanks in advanced!
Haim