get longest orf from emboss getorf

crayfish · 12-09-2013, 08:04 PM

Hi, i use emboss getorf to extract orf, while i only want one longest sequences in my file, is there any available software of script can do this?

maubp · 12-11-2013, 10:31 AM

I wrote a Python script (using Biopython) similar to getorf which has the option of returning all the longest ORFs (or the first longest ORF) in each sequence. This subtle distinction allows for the fact there may not be a single unique longest ORF, there could be several equally long ORFs.

It is available with a Galaxy wrapper here on the Galaxy Tool Shed:
http://toolshed.g2.bx.psu.edu/view/p...t_orfs_or_cdss

Or, directly from GitHub:
https://github.com/peterjc/pico_gala...rfs_or_cdss.py

crayfish · 12-12-2013, 09:07 AM

Thanks a lot , maubp

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12-09-2013, 08:04 PM	#1
crayfish Junior Member Location: usa Join Date: May 2012 Posts: 7	get longest orf from emboss getorf Hi, i use emboss getorf to extract orf, while i only want one longest sequences in my file, is there any available software of script can do this?

12-11-2013, 10:31 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	I wrote a Python script (using Biopython) similar to getorf which has the option of returning all the longest ORFs (or the first longest ORF) in each sequence. This subtle distinction allows for the fact there may not be a single unique longest ORF, there could be several equally long ORFs. It is available with a Galaxy wrapper here on the Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/view/p...t_orfs_or_cdss Or, directly from GitHub: https://github.com/peterjc/pico_gala...rfs_or_cdss.py

12-12-2013, 09:07 AM	#3
crayfish Junior Member Location: usa Join Date: May 2012 Posts: 7	Thanks a lot , maubp