getOrfs {GeneR}R Documentation

Gets ORFs from a sequence

Description

Gets ORFs (Open Reading Frames) from a sequence.

Usage

getOrfs(phase = NULL,seqno=0,start="atg",
                   stop=c("taa","tag","tga"), complete = TRUE,suborfs=TRUE)
maxOrf(seqno=0,phase = NULL,start="atg",
                   stop=c("taa","tag","tga"), complete = TRUE)

Arguments

seqno

Integer/scalar, Sequence number (buffer number)

phase

Integer/scalar,. 1,2 or 3, NULL for all three phases

start

string/vector, start codons

stop

string/vector, stop codons

complete

Flag: true returns only complet Orfs, else return all Orfs.

suborfs

Flag: true returns all orfs including subparts of a large orf if it exists "atg" in the phase. False: does not returns sub-orfs.

Value

getOrf returns a table of positions. NULL if no Orfs.

maxOrf returns the size of the largest Orf, -1 if no Orf.

All functions return NA if error.

Note

Reverse strand : not implemented

Author(s)

A. Lucas, Emna Marrakchi and Vincent Lefort

Examples

s<-"gtcatgcatgctaggtgacagttaaaatgcgtctaggtgacagtctaacaa"
placeString(s)

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


# To get all ORFs on the reverse strand:
sc <- getSeq(0,1)
placeString(sc,seqno=1)
getOrfs(phase = NULL,seqno=1)

# All orfs on both strands :
rbind(getOrfs(seqno=0),getOrfs(seqno=1))

[Package GeneR version 2.24.0 Index]