findHomolog: This function compares all overlapping ORFs with the Scer ORF...
In oacar/synal: Synteny Alignment and Analysis for Saccharomyces sensu stricto

This function compares all overlapping ORFs with the Scer ORF and saves best ORF in terms of number of AAs (highest number of identical aminoacids)

1 2	findHomolog(DNAStr, aa_alignment, start, stop, ygeneSeq, types, outputDirectory = NULL, orfName, best = FALSE)

`DNAStr`	aligned DNAStringSet with all sequences (including the ORF to be searched) in it, this is the full syntenic block not subalignment
`aa_alignment`	Amino acid alignment over the subalignment
`start`	start codon position of ygeneSeq in DNAStr
`stop`	last nucleotide position of ygeneSeq in DNAStr
`ygeneSeq`	sequence of interest
`types`	this is a vector which contains the species names in the alignment for writing correct output files
`outputDirectory`	path for files to be written in
`orfName`	ORF identifier name that will be used for file writing
`best`	should the function returns all overlapping ORFs or only the best one

nothing returns at the moment, all files are written in path with 3 files for each species. pairwise nucleotide alignment, pairwise AA alignment and pairwise AA alignment that shows only overlap of two ORFs

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