- HMM_build
- Usage:
HMM_build <train set> <profile outfile>
- Parameters
in HMM_build.h file that must be set before running the program
- Example:
HMM_build ntrain ntrainprofile
- In
this case, num_indices=3 and DOMAIN_NUM=12
- If <train
set> = ntrain, it means you must have the fasta format files
ntrain.d1,ntrain.d2……ntrain.d12
- ntrain.d1
contains training sequences of domain 1
- There
must exist a file named “index36.out” which contains the indices for
each domain. The indices come in sets of num_indices (that is 3 in this
case). First set corresponds to indices used for domain 1, second set
for domain 2, so on.
- HMM_run
- Usage:
HMM_run <profile file> <test file> <result file>
- Example:
HMM_run ntrainprofile yeast.fasta yeast_result.txt
- ntrainprofile
is the profile that you have obtained by running HMM_build
- yeast.fasta
contains the test sequences in fasta format
- yeast_result.txt
is the output file containing scores obtained by running HMM_run
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