align.MEME: Multiple sequence alignment by means of MEME.

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/align.MEME.R

Description

DNA sequences are aligned by means of MEME Version 4.4.0. (Multiple Expectation-Maximization for Motif Elicitation)

Usage

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align.MEME(filein, fileout = "Sq.fa", iicc)

Arguments

filein

A set of nucleotide sequences in FASTA format.

fileout

Output file in FASTA format

iicc

A list of argument input.

Details

This function needs aaMI-package. This funtions works with meme<=4.3.0

Value

Output is a file in FASTA format with aligned nucleotide sequences.

Author(s)

Erola Pairo <[email protected]> and Joan Maynou <[email protected]>

References

T. Bailey and C. Elkan, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, in Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, August 1994,

See Also

align.clustalw, align.MUSCLE

Examples

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iicc<-vector(mode="list",length=4)
iicc$nummotif<-c(1,2)
iicc$lenmotif<-c(10,11,12)
iicc$call.meme<-"./meme"
pathMEET<-system.file("exdata",package="MEET")
#align.MEME(filein=paste(pathMEET,"AP1.fa",sep="/"),fileout="Sq.fa",iicc)

MEET documentation built on May 31, 2017, 4:10 a.m.