Question

Best command line ORF finder

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6.2 years ago

dylan.lawrence ▴ 90

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.)

orf command line software • 10k views

ADD COMMENT • link updated 4.8 years ago by emilyc ▴ 30 • written 6.2 years ago by dylan.lawrence ▴ 90

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For fasta EMBOSS getORF and transeq.

ADD REPLY • link 6.2 years ago by GenoMax 141k

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

ADD REPLY • link 6.2 years ago by dylan.lawrence ▴ 90

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

ADD REPLY • link 6.2 years ago by GenoMax 141k

score 2 · Answer 1 · 2019-07-17

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4.8 years ago

hauken_heyken ▴ 130

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

ADD COMMENT • link 4.8 years ago by hauken_heyken ▴ 130

score 0 · Answer 2 · 2019-07-17

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4.8 years ago

emilyc ▴ 30

GeneMark (many options for different needs).

ADD COMMENT • link 4.8 years ago by emilyc ▴ 30