Biomedical Computation


Usage: mhmme [options] <HMM filename>

Description: Given a MEME Suite hidden Markov model (HMM), mhmme randomly generates sequence from the model and prints them in FASTA format.

Input: <HMM file> – An HMM in Meta-MEME format must be provided. If the filename is given as ‘-‘, then ‘mhmme’ will attempt to read the HMM from standard input.

Output: The mhmme program prints to standard output one or more sequences in Fasta format.


Option Description and default behavior
–occurs Rather than printing the raw sequence, print a pseudo-sequence in which non-motif regions are represented as hyphens and motifs are represented like this: *____7___*, where 7 is the motif index. The output is normal FASTA format.
–seed Set the seed for the random number generator. The seed is set from the clock.
–numseq The number of sequences to emit. One sequence is generated.