Combine multilple genome to one genome
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5.4 years ago
l0o0 ▴ 210

I have a question about how to combine multiple genomes from different rice species to one genome. These rice species have close genetic relationship. I knon this question sounds weird, but I really want to find ways to combine these genomes.

At first glance of this question, I will blast A genome sequence with B genome. According the blast result, the unmatch sequence may be different with B genome and insert these unmatch sequences in A genome. But I don't know the insert position. This is a simple idea in my mind now. I would be very grateful if you can give me some suggestions.

genome • 1.4k views
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I have just one question: Why?

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Now I have 5 genomes from different rice specie. If there would be a combination of genome, it will easy and fast to find some interesting region. It is just a lazy way.

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No, it's an indication that to make a job technically "easier", the bigger picture has been forgotten. I don't think this is a valid approach.

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There may be other, simpler ways to approach the question you're interested in. For evolutionary studies, you may want to consider reconstructing an ancestral genome. Otherwise, to combine genomes, I think the genome graph representation would be the best approach.

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Thank you for your advice, I will find some resources about genome graph representation.

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Would a multiple sequence alignment make sense, followed by calling consensus?

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Yes, I will try to make a genome consensus sequence by alignments ;)

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