Entering edit mode
6.2 years ago
l0o0 ▴ 220
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.
I have just one question: Why?
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.
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.
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.
Thank you for your advice, I will find some resources about genome graph representation.
Would a multiple sequence alignment make sense, followed by calling consensus?
Yes, I will try to make a genome consensus sequence by alignments ;)