AllOrfs {GeneR} | R Documentation |
Get ORFs (Open Reading Frame) from a sequence. Codon start is atg, stop is taa,tga,tag.
allOrfs(phase = NULL,seqno=0,start="atg", stop=c("taa","tag","tga")) maxOrf(seqno=0,phase = NULL,start="atg", stop=c("taa","tag","tga"))
seqno |
Integer. Sequence number (bufseq) |
phase |
Integer. 1,2 or 3, NULL for all phases |
start |
"start" sequences |
stop |
"stop" sequences |
allOrf return a table. NULL if no Orfs.
maxOrf return size of largest Orf, -1 if no Orf.
All functions return NA if error.
A. Lucas and Vincent Lefort
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))