How To Determine The Core Genome From The Orthomcl Output

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12.7 years ago

Juliana Soto ▴ 50

Dear All, I used Orthomcl to identify the core genome of 31 bacterial genomes.

I would like to know how can I extract the genes present in all the genomes from the groups.txt file which has all the ortholog groups of the 31 genomes. I need to identify all the genes that are shared by the 31 genomes.

there is a way to do this other than manually?

thanks, best regards

genome orthomcl orthologues • 4.3k views

ADD COMMENT • link updated 7.0 years ago by Biostar 20 • written 12.7 years ago by Juliana Soto ▴ 50

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We need to see what groups.txt looks like to answer this. Can you post a small portion of it, or a detailed description of the format?

ADD REPLY • link 12.7 years ago by Neilfws 49k

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Hi. Sorry for digging up an old post. I was just wondering has anybody solved this? I was wondering the same thing and wasn't sure if I should post a new question when this ones exists.

ADD REPLY • link 10.8 years ago by Lisa ▴ 330

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Since the author declined to improve their question, I don't see why you cannot post a new one, so long as you provide the required details that they did not :)