Question: MAUVE - genome alignment
1
gravatar for glady
2.6 years ago by
glady240
glady240 wrote:

Hi everyone, I have used MAUVE for creating a genome alignment of 7 pseudomonas genomes. The alignment has been completed and I have got a image showing LCB's. But I want to find the orthologus regions which are present in these genomes. I am trying to export this file with the help of 'Export orthologus', this command is creating a output file, but file created by it is empty. Can someone help me with this, if I am going wrong somewhere?

Thank you in advance.

genome • 1.6k views
ADD COMMENTlink modified 2.6 years ago by sentausa630 • written 2.6 years ago by glady240
2

I suggest that you search the Mauve support list located here. Example search for your question.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax64k

What exactly do you want to get? What do you mean by saying that you "want to find the orthologus regions which are present in these genomes"? I'm sensing that you're not doing the correct approach by using Mauve.

ADD REPLYlink written 2.6 years ago by sentausa630

I want MAUVE (progressiveMAUVE) to detect orthologs which are common between the genomes. MAUVE does give you a option to download these orthologs file -> when you select 'Exoprt ortholog' from the Tools menu. When I am performing these steps an output file is getting created, but the output file created is empty (0 kb). What should I do ? Is there something wrong ? or is there any other way of generating the orthologs file ?

ADD REPLYlink written 2.6 years ago by glady240

And why do you want to detect orthologs which are common between the genomes? What do you mean by orthologs here? Orthologous genes? And if you have them, what will you do to them? I just want to know what you really want to do so that I can help you, not necessarily using Mauve.

ADD REPLYlink written 2.6 years ago by sentausa630

I am doing a comparative genome analysis study between two bacterial genomes and for this I am using MAUVE to perform genome alignment. So, that it can detect certain orthologus clusters between those genomes.

ADD REPLYlink written 2.6 years ago by glady240

What do you mean with orthologous "clusters"? Orthologous genes? You can use other tools like OrthoMCL, Proteinortho, or OrthoFinder to find orthologous genes between genomes, and it's more effective than using Mauve.

ADD REPLYlink written 2.6 years ago by sentausa630

okay, I will try them. thank you.

ADD REPLYlink written 2.6 years ago by glady240
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