As well as finding motifs, STEME is able to scan genomic sequences for instances of these motifs (putative transcription factor binding sites). To use STEME as a motif finder you can execute the following command:
steme-pwm-scan --prediction-Z-threshold=.5 --lambda=.001 <motifs file> <input fasta sequence file>
which will create a file called steme-pwm-scan.out containing the positions of the putative binding sites and their scores. The motifs file should be in minimal MEME format (STEME will output a file in this format called steme.txt). The --prediction-Z-threshold option sets the minimum score for which predictions are reported. The --lambda option determines the model hyper-parameter that dictates how likely binding sites are. Think of lambda as a per-base probability of a binding site so --lambda=.001 states that a priori we expect one binding site per 1000 base pairs. Given this lambda, the Z score for a motif instance can be read as the probability that this is a binding site for the transcription factor.
STEME’s PWM scanning algorithm is very efficient on large sequence sets due to its use of a suffix tree. In fact given enough memory STEME can scan whole genomes for motif instances. If you are scanning 256 or fewer sequences some advantage can be gained by defining the environment variable STEME_USE_GENOME_INDEX=1 before running steme-pwm-scan. STEME will use a different genome optimised suffix tree with smaller memory requirements than the default one. In our experiments we found that scanning the mouse genome required about 40Gb of main memory in this case. When STEME starts you will see a message detailing limits on the suffix tree in terms of number of sequences, individual sequence length and total sequence length. The default suffix tree reports:
Loaded standard version of STEME C++-python interface: max seqs=4294967296; max seq length=4294967296; max total length=4294967296
the genome optimised version reports:
Loaded genome version of STEME C++-python interface: max seqs=256; max seq length=4294967296; max total length=4294967296
Transcription factors can bind to DNA in complexes. Oftentimes their binding sites must be a fixed distance apart for these complexes to form. Given a set of putative transcription factor binding sites, STEME can analyse them for enriched spacings of pairs of motifs. Highly enriched spacings suggest that a pair of transcription factors act in tandem:
steme-spacing-analysis -d <distance> -t <threshold on log evidence>
will run STEME’s spacing analysis method producing a list of results like:
Here we can see that instances of the pair of motifs TCCCA-ReChIP and GCCACC-ReChIP occurred 5,223 times at a distance of less than 20 base pairs. There is an obvious enrichment where an instance of the reverse complement of GCCACC-ReChIP is 2 or 3 base pairs before an instance of TCCCA-ReChIP. Given the 5,223 pairs of instances of these motifs the log evidence in favour of an enriched distribution is large: 711.8.
Given that you have identified a pair of motifs that have some enriched spacing, you may wish to locate instances of the motifs at this spacing. STEME provides a script to do just this:
steme-find-spacings <spacing definitions file>
The spacing definitions file should contain a list of spacings that you are interested in. For example:
TCCCA-ReChIP GCCACC-ReChIP C D 2
TCCCA-ReChIP GCCACC-ReChIP C D 3
would find reverse complemented (C) instances of GCCACC-ReChIP 2 or 3 base pairs downstream (D) of TCCCA-ReChIP instances.