Best command line ORF finder

Question

[dylan.lawrence]

I am currently using the NCBI Orf Finder website which works great, but I want to automate my pipeline a bit more and am trying to find a good command line based Orf Finder. I tried to download the NCBI version but they only provide a pre-compiled version which the server I use is a missing a library for.

Does anyone have a good suggestion for a command line based orf finder that can take in a DNA fasta/fastq and output all proteins found in the DNA sequence? (Of all six frames.)

[GenoMax]

For fasta EMBOSS getORF and transeq.

[dylan.lawrence]

How exactly do I download getORF... I have looked all over the website and it is not obvious to me where it is.

[GenoMax]

Download EMBOSS source here. sixpack is another EMBOSS program that you can use for 6 frame translations.

Answer 1

[hauken_heyken]

The R package ORFik in Bioconductor has all you need, implemented in C++ and even takes circular genomes.

Answer 2

[emilyc]

GeneMark (many options for different needs).