hmmbuild {MethTargetedNGS} | R Documentation |
This function creates profile hidden markov model of the given aligned sequences using HMMER algorithm.[1]
hmmbuild(file_seq, file_out,pathHMMER="")
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/) |
Create Profile Hidden Markov Model in local directory
Require HMMER software
Windows User: Please download HMMER from http://hmmer.janelia.org/
Setup cygwin from http://www.cygwin.com
Linux/Mac User: Download binaries or compile HMMER from http://hmmer.janelia.org/
Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri
Maintainer: Muhammad Ahmer Jamil engr.ahmerjamil@gmail.com
[1]Finn, Robert D., Jody Clements, and Sean R. Eddy. "HMMER web server: interactive sequence similarity searching." Nucleic acids research (2011): gkr367.
msa = system.file("extdata", "msa.fasta", package = "MethTargetedNGS") if (file.exists("/usr/bin/hmmbuild")) hmmbuild(file_seq=msa,file_out="hmm",pathHMMER = "/usr/bin")