OrfM

A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences.

Install

OrfM can be installed in 3 ways.

1) Install from pre-compiled binaries

OrfM can be installed by downloading pre-compiled binaries available at https://github.com/wwood/OrfM/releases. Once you have downloaded the package, extract and run it e.g. for GNU/Linux:

tar xzf orfm-x.x.x_Linux_x86_64.tar.gz
cd orfm-x.x.x_Linux_x86_64
./orfm -h

2) Install from source

If you desire, OrfM can also be installed from source. Download the orfm-x.x.x.tar.gz from the releases page (not the 'Source code' or the 'Download zip') and then follow the usual protocol for compilation and installation:

tar xzf orfm-x.x.x.tar.gz
cd orfm-x.x.x
./configure
make

To run make check you need Ruby and as well as the rspec and bio-commandeer rubygems. This step is optional.

gem install rspec bio-commandeer # may require 'sudo'
make check

Then finally to install OrfM

sudo make install
orfm -h

3) Install with GNU Guix

Or, you can install through guix:

guix package -i orfm

4) Install with brew

Thanks to Torsten Seemann (@tseemann), OrfM can be installed through homebrew:

brew install brewsci/bio/orfm

Running

To find all reading frames greater than 96 nucleotides in length:

orfm <seq_file> >orfs.fa

The <seq_file> can be a FASTA or FASTQ file, gzipped or uncompressed. The default is 96 because this is the correct number for 100bp so that each of the 6 frames can be translated. Using 99 would mean that the third frame forward (and the corresponding reverse frame) cannot possibly returned as an ORF because this would entail it encapsulating bases 2-101, and 101>100.

Output

The output ORFs fasta file contains any stretch of continuous codons which does not include a stop codon. There is no requirement for a start codon to be included in the ORF. One could say that OrfM is an ORF caller, not a gene caller (like say prodigal or genscan).

The output ORFs are named in a straitforward manner. The name of the sequence (i.e. anything before a space) is followed by _startPosition_frameNumber_orfNumber and then the comment of the sequence (i.e. anything after the space) is given after a space, if one exists. For example,

$ cat eg.fasta
>abc|123|name some comment
ATGTTA
$ orfm -m 3 eg.fasta
>abc|123|name_1_1_1 some comment
ML

The startPosition of reverse frames is the left-most position in the original sequence, not the codon where the ORF starts.

Not too slow

It runs in reasonable time compared to e.g. translate from Sean Eddy's squid (available as part of the Ubuntu biosquid package), getorf from the emboss toolkit, and prodigal, a more nuanced gene caller. For a 463MB fasta file of 100bp sequences:

orfm -m 96 the.fa >orfm.fa
  #=> 7 seconds

translate -l 32 the.fa >biosquid.m33.txt
  #=> 29 seconds
  
getorf -sequence the.fa -minsize 96 -outseq getorf.fa
  #=> 38 sec

pigz -cd 110811_E_1_D_nesoni_single.fq.gz |fq2fa |prodigal -q -p meta -i /dev/stdin -a 110811_E_1_D_nesoni_single.prodigal.faa -o /dev/null
  #=> 16 min 6 sec

translate also does not appear to be able to handle fastq files (even piped in on stdin as fasta), and does not output a standard FASTA format file.

FAQ

bash: ./configure: No such file or directory

This can happen when trying to build OrfM from source. It might mean that the original source code has been downloaded, rather than the 'dist' archive. Download orfm-x.x.x.tar.gz from the releases page which contains the configure script (not the 'Source code'), and then follow the instructions for building from source above.

Contributing to OrfM

Patches most welcome. To get started:

git clone --recursive https://github.com/wwood/OrfM
cd OrfM
./autogen.sh
./configure
make check

Credits

Compiled into the code is kseq.h from seqtk and an implementation of the Alo-Corasick algorithm from strmat modified slightly. Both are MIT licenced. A few GNU libc libraries are used too.

Citing OrfM

Software (c) Ben J. Woodcroft, released under LGPL - see the LICENSE.txt for licensing details.

A peer-reviewed manuscript describing OrfM has been published. If you use OrfM in your work then please help us out by citing it - thank you.

Ben J. Woodcroft, Joel A. Boyd, and Gene W. Tyson. OrfM: A fast open reading frame predictor for metagenomic data. (2016). Bioinformatics. doi:10.1093/bioinformatics/btw241.