AllOrfs {GeneR}R Documentation

Get ORFs from a sequence

Description

Get ORFs (Open Reading Frame) from a sequence. Codon start is atg, stop is taa,tga,tag.

Usage

allOrfs(phase = NULL,seqno=0,start="atg",
                   stop=c("taa","tag","tga"))
maxOrf(seqno=0,phase = NULL,start="atg",
                   stop=c("taa","tag","tga"))

Arguments

seqno Integer. Sequence number (bufseq)
phase Integer. 1,2 or 3, NULL for all phases
start "start" sequences
stop "stop" sequences

Value

allOrf return a table. NULL if no Orfs.
maxOrf return size of largest Orf, -1 if no Orf.
All functions return NA if error.

Author(s)

A. Lucas and Vincent Lefort

Examples

s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
placeString(s)

allOrfs(phase = NULL,seqno=0)
maxOrf()

# On complemetary strand:
sc <- getSeq(0,1)
placeString(sc,seqno=1)
allOrfs(phase = NULL,seqno=1)

# All orfs :
rbind(allOrfs(seqno=0),allOrfs(seqno=1))

[Package GeneR version 1.4.2 Index]