align: Gets DNAStringSet aligns it

In oacar/synal: Synteny Alignment and Analysis for Saccharomyces sensu stricto

Description

Gets DNAStringSet aligns it

Usage

align(mySequences, orfName, outputDirectory = NULL, ygeneSeq = NULL,
  algorithm = "Muscle")

Arguments

mySequences	DNAStringSet with all sequences in it
orfName	ORF identifier name that will be used for file writing
outputDirectory	path for files to be written in
ygeneSeq	sequence of ORF of interest. If not given, last sequence of mySequences considered to be ygeneSeq
algorithm	alignment algorithm to be used. Default is 'Muscle' but 'ClustalW' and 'ClustalOmega' are available

Value

aligned DNAStringset, start and stop positions of orfName on DNAStringSet and AA alignment of the orfName sequence with other species

oacar/synal documentation built on Feb. 22, 2020, 1:42 p.m.