MAUVE - genome alignment
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7.6 years ago
glady ▴ 320

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 • 4.2k views
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I suggest that you search the Mauve support list located here. Example search for your question.

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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.

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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 ?

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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.

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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.

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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.

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okay, I will try them. thank you.

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