MethTargetedNGS (version 1.4.0)

hmmbuild: Create Profile Hidden Markov Model of given aligned sequences

Description

This function creates profile hidden markov model of the given aligned sequences using HMMER algorithm.[1]

Usage

hmmbuild(file_seq, file_out,pathHMMER="")

Arguments

file_seq

Multiple sequence aligned fasta file

file_out

Output hidden markov model file

pathHMMER

Path where HMMER software is installed. Note: Windows user must setup cygwin to use this feature and set path to HMMER binaries ( ~hmmer/binaries/)

Value

Create Profile Hidden Markov Model in local directory

References

[1]Finn, Robert D., Jody Clements, and Sean R. Eddy. "HMMER web server: interactive sequence similarity searching." Nucleic acids research (2011): gkr367.

See Also

nhmmer

Examples

msa = system.file("extdata", "msa.fasta", package = "MethTargetedNGS")
if (file.exists("/usr/bin/hmmbuild"))
  hmmbuild(file_seq=msa,file_out="hmm",pathHMMER = "/usr/bin")