MethTargetedNGS (version 1.4.0)

nhmmer: Calculate likelihood of the given profile hidden markov model against group of sequences

Description

This function calculates likelihood score of given pool of sequences against given profile hidden markov model using HMMER algorithm.[1]

Usage

nhmmer(file_hmm, file_seq, pathHMMER="")

Arguments

file_hmm

HMM file from hmmbuild function

file_seq

Sequence fasta file for calculating likelihood

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

Matrix containing likelihood scores

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

hmmbuild

Examples

msa = system.file("extdata", "msa.fasta", package = "MethTargetedNGS")
tumor = system.file("extdata", "Tumor.fasta", package = "MethTargetedNGS")
if (file.exists("/usr/bin/hmmbuild"))
{hmmbuild(file_seq=msa,file_out="hmm",pathHMMER = "/usr/bin")
res <- nhmmer("hmm",tumor,pathHMMER = "/usr/bin")
res}