checkORF: Check Orf

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

Description

Checks if Amino Acid sequence has M — X or I — X ORF by using regular expressions. This can be changed to only check M — X ORF, or for any other start codons

Usage

checkORF(aa_seq)

Arguments

aa_seq

Aminoacid sequence as character string. Change it by as.character if using AAString

Value

if there is an ORF then return TRUE If there is no ORF check what is missing an M or X If M is missing return 'M' — if X is missing return 'X' — if both are missing return 'BOTH', if there is not orf but X —- M sequence, it will return 'Neither'

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