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

Value

Create Profile Hidden Markov Model in local directory

Note

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/

Author(s)

Muhammad Ahmer Jamil, Prof. Holger Frohlich, Priv.-Doz. Dr. Osman El-Maarri

Maintainer: Muhammad Ahmer Jamil engr.ahmerjamil@gmail.com

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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(MethTargetedNGS)
Loading required package: stringr
Loading required package: seqinr
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:gplots':

    space

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:seqinr':

    translate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MethTargetedNGS/hmmbuild.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hmmbuild
> ### Title: Create Profile Hidden Markov Model of given aligned sequences
> ### Aliases: hmmbuild
> ### Keywords: ProfileHMM hmmbuild
> 
> ### ** 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")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>