ORFFinder

ORFFinder in Python. Inspired by NCBI's version: https://www.ncbi.nlm.nih.gov/orffinder/

Finds the open reading frame (6-frame scan) on a given 5' to 3' nucleotide.

Installation:

pip3 install orffinder

Terminal Usage

Three command-line executable commands are available: orffinder-to-gtf orffinder-to-sequence and orffinder-to-gff3.

Documentation for these commands can be retrieved by specifying <command> -h.

API Usage

Import the package

IMPORTANT: Your DNA/RNA strand should always be from the 5' to 3' direction when input! (Image credit: Khan Academy)

from Bio import SeqIO
from orffinder import orffinder

sequence = SeqIO.read("gene.fasta", "fasta")
orffinder.getORFs(sequence, minimum_length=75, remove_nested=True)

Documentation

getORFs()

Returns the loci of discovered ORFs in a dictionary format.

sequence: sequence in Biopython Seq or String format.
minimum_length: minimum size of ORF in nucleotides. Default: 75
start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"]
stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"]
remove_nested: remove all ORFs completely encased in another. Default: False
trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False

getORFNucleotides()

Returns a list of Biopython Seq objects or loci of discovered ORFs with Biopython Seq objects in a dictionary format.

sequence: sequence in Biopython Seq or String format.
return_loci: return the loci together with the nucleotide sequences. Default: False
minimum_length: minimum size of ORF in nucleotides. Default: 75
start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"]
stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"]
remove_nested: remove all ORFs completely encased in another. Default: False
trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False

getORFProteins()

Returns a list of Biopython Seq objects or loci of discovered ORFs with Biopython Seq objects in a dictionary format.

sequence: sequence in Biopython Seq or String format.
translation_table: translation table as per BioPython. Default: 1
return_loci: return the loci together with the protein sequences. Default: False
minimum_length: minimum size of ORF in nucleotides. Default: 75
start_codons: recognised 3-base-pair codons for initialisation. Default: ["ATG"]
stop_codons: recognised 3-base pair condons for termination. Default: ["TAA", "TAG", "TGA"]
remove_nested: remove all ORFs completely encased in another. Default: False
trim_trailing: remove ORFs are the edge of the sequence that do not have a defined stop codon. Default: False

Dependencies