maxORF {ftrCOOL}

Maximum Open Reading Frame in DNA (maxORF)

Description

This function gets a sequence as the input. If reverse is true, the function extracts the max Open Reading Frame in the sequence and its reverse complement (hint: Six frames). Otherwise, only the sequence is searched (hint: Three frames).

Usage

maxORF(seqs, reverse = TRUE, label = c())

Arguments

seqs

is a FASTA file containing nucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a nucleotide sequence.

reverse

It is a logical parameter which assumes the reverse complement of the sequence.

label

is an optional parameter. It is a vector whose length is equivalent to the number of sequences. It shows the class of each entry (i.e., sequence).

Value

A vector containing a subsequence for each given sequences. The subsequence is the maximum ORF of the sequence.

Note

If a sequence does not contain ORF, the function deletes the sequence.

Examples

fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
ORF<-maxORF(seqs=fileLNC,reverse=FALSE)