findBestOverlap: Finds best overlapping ORF in terms of the number of...
In oacar/synal: Synteny Alignment and Analysis for Saccharomyces sensu stricto

Finds best overlapping ORF in terms of the number of identical aminoacids

1 2	findBestOverlap(DNAStr, j, start, stop, ygeneSeq, types, map_ygene = NULL)

`DNAStr`	DNA alignment of syntenic block. This is the full alignment not subalignment
`j`	this is the iterator for the ID of species of interest on DNAStr and types vector
`start`	start position of ATG of proto-gene on DNAStr
`stop`	last nucleotide position of proto-gene on DNAStr
`ygeneSeq`	proto-gene sequence without gaps. This is used for determining the frame of proto-gene with respect to the aligned other species ORF
`types`	this is used for names. by default c('Spar','Smik','Skud','Sbay')
`map_ygene`	this is the map between aligned and original sequence of ORF of interest

list of three elements

dna = dna alignment of jth species orf with proto-gene, aa = aa alignment with full jth ORF, aaOverlap = overlapping regions of both ORFs(translated), dnaOverlap=overlapping regions of both ORFs

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