Question: Best command line ORF finder
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gravatar for dylan.lawrence
2.3 years ago by
dylan.lawrence20 wrote:

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.)

command line orf software • 4.3k views
ADD COMMENTlink modified 10 months ago by emilyc10 • written 2.3 years ago by dylan.lawrence20
1

For fasta EMBOSS getORF and transeq.

ADD REPLYlink written 2.3 years ago by genomax83k

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

ADD REPLYlink written 2.3 years ago by dylan.lawrence20

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax83k
0
gravatar for hauken_heyken
10 months ago by
hauken_heyken40 wrote:

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

ADD COMMENTlink written 10 months ago by hauken_heyken40
0
gravatar for emilyc
10 months ago by
emilyc10
emilyc10 wrote:

GeneMark (many options for different needs).

ADD COMMENTlink written 10 months ago by emilyc10
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