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Generating likely sequences: hmme

For debugging purposes, or simply to verify that an HMM captured a good consensus, you can use the program hmme to emit sequences according to the statistics of the model. hmme will print them out in SELEX alignment format so they're easy to look at and compare.

> hmme globin2.hmm

By default, 10 sequences will be generated; you can make more or less using the -n <num> option. The -f option may be specified to force unaligned FASTA output instead of SELEX alignment format.

The output will be sent to your terminal. If you want to save the sequences in a file instead, specify the file name with the -o option:

> hmme -o random_globins.out globin2.hmm

hmme -b globin2.hmm will instead emit the single most probable sequence from the model. You might think of this as the ``consensus sequence''.



Sean Eddy
Mon Apr 17 09:54:19 CDT 1995