I am using MEME suite to find some information about TF motif site from a list of TSS upstream sequence that I got. The DNA sequence is generated from a non-model organism, which is also a crustacean. As I dont have a control set, I simply input with the "primary sequence (fasta sequence)" and "output from MEME (motif that I am interested)" to do the local enrichment with option "anywhere". I got some output with most of it showed e-value as 1 and p-value as 9. This doesn't seemed good instead of using "MEME output", I swapped it with fly database, yet it produced nothing. I have also tried with eukaryote database, JASPAR2018_core_vertebrate and jaspar2018_core_insect, they all showed nothing in the output. Is there any advise on how to make this motif findings meaningful using CentriMo? I know that simply relying on the output of MEME is not enough because many false positives results is generated at the same time. Instead of MEME if I straight away proceed with TOMTOM, is this makes sense since I can argue that the sequence called by MEME showed high similarity to consensus sequence found by TOMTOM? Thank you in advance.
What is the predicted motif length by MEME. To check the short motif enrichment you can use STREME (DREME is deprecated).
Thanks for the reply. I have multiple files which contain different sequences which represents different gene sets. While each files has more than 100 sequences(each sequence 3k bases), STREME gives me a list of motif discovered for each file ( default setting 8-15 for length). Since they are already enriched, I guess the next step is to examine them with TOMTOM and skip CentriMo?
TOMTOM and CentriMo, serve different purposes. TOMTOM is for aligning the predicted motifs with known motifs (you can relate it with a BLAST in sequence alignment) and find out the similarity whereas CentriMo predicts the density of the given motif in a specific region of the target sequence.
Let's say TOMTOM gives you an idea about the class/type of the motif whereas CentriMo gives you a gist of how that motif is distributed in your sequence.