246    ◾    Bioinformatics

DREME is depreciated by the developer. So, it is recommended to use MEME or

STREME instead. Since we wish to find motifs in more than 50 FASTA sequences, we will

use STREME program. STREME will attempt to find motifs by iterating five steps until the

user-specified stopping criterion is met. The stopping criterion can be either the p-value of

the motif or the total number of motifs found. The five steps include building of a suffix

tree for both the ChIP-Seq FASTA sequences and control sequences, evaluation of the seed

words, motif refinement, motif significance computation, and motif erasing (converting

the site of the best motif to N in the primary sequences and control sequences).

The following STREME command searches for motifs in the FASTA sequences of the

three ChIP-Seq samples:

streme --p chip1_peaks.fasta \

--oc streme_motifs_chip1 \

--dna \

--thresh 0.05

streme --p chip2_peaks.fasta \

--oc streme_motifs_chip2 \

--dna \

--thresh 0.05

FIGURE 6.19  The motifs found by DREME.