changeATCG: Nucleotide conversion for the gene from minus strand

In hongzhonglu/Yeastspot3D: Mutation mapping analysis with protein 3D structure for yeast

Description

changeATCG should be used to firstly,if the cds from the minus strand get the mutation information on the minus strand based on that from the positive strand The followed exlain that why we need changeATCG for gene from minus strand Both + and - strands have 5'-3' and 3'-5' directions, however, the genomic coordinates refer to only the 5'-3' direction of the reference, +, strand. Your second statement is indeed correct. Another illustrative example, if you want to find the transcription start site (TSS) of a gene that spans the region of (in genomic coordinates) 10800 to 11200 in, say, chromosome 11, then you should also consider which strand the gene is located in. Let's say the base at 10800 is A and the base at 11200 is C. If the gene is in the + strand, than 10800-11200 refer to the 5'-3' of the gene, hence the TSS is 10800 A. If the genes is in the - strand, then 10800-11200 (always for + strand) corresponds to the 3'-5' direction of the gene located in the complementary strand, hence the TSS is 11200 G (complementar to C).

Usage

changeATCG(ss)

Arguments

ss	A kind of nucleotide

Value

A string of complementary nucleotide

Examples

changeATCG(ss="A")
changeATCG(ss="C")
changeATCG(ss="T")
changeATCG(ss="G")

hongzhonglu/Yeastspot3D documentation built on March 28, 2020, 6:06 p.m.