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

In MEET: MEET: Motif Elements Estimation Toolkit

Description

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

Usage

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 <[e-mail]> and Joan Maynou <[e-mail]>

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

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 2, 2019, 5:52 p.m.