alignWoSmorf: Align syntenic blocks This function take align syntenic...

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

Description

Align syntenic blocks This function take align syntenic blocks and then searches for proto-gene sequence on the Scer sequence using regular expressions

Usage

alignWoSmorf(sequenceSet, algorithm = "Muscle", smorfSeq = NULL,
  aligned = F)

Arguments

sequenceSet	The sequences of syntenic blocks as DNAStringSet object. At leas 3 sequences are needed and last sequence should be the proto-gene
algorithm	this function uses msa package for alignment which can use c("ClustalW", "ClustalOmega", "Muscle") as alignment algorithms. I used 'Muscle' as default. There is also standalone muscle package which is also used in this package
smorfSeq	if this is given, the sequenceSet is taken as full syntenic blocks, if not the last sequence of the sequenceSet is taken as the orf of interest sequence
aligned	if this is TRUE, then the given sequences will be taken as aligned, so no realignment will be applied.

Value

list of alignment object as DNAStringSet with start and stop positions of proto-gene ORF on the aligned Scer sequence

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