How can I map coordinates between two strains of yeast?
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12 weeks ago
Jimmy ▴ 30

I have two fasta files of genome sequences of two different strains of yeast. I'm looking for a way to map coordinates between these two strains. The reason is that I want to download and use some data from the SGD database for a strain other than the one I am working with and add it as a predictor to a neural network for an aspect of the genome of the yeast strain that I am working with. How can I do this?

coordinates yeast genome mapping fasta • 501 views
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genome sequences of two different strains of yeast

Are they the same species?

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Yes (S. cerevisiae)

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12 weeks ago
dthorbur ★ 1.4k

It sounds like you are looking for synteny between the two genomes. I'm assuming they are assembled, but that may not be the case. If so, here is a review of available tools from 2018. I'm sure there is a more recent review, but it gives you an idea of what is involved.

Do you have annotations for these genomes? That would permit anchored synteny approaches. If not, you might need something like Satsuma2 which is a kmer alignment based synteny tool.

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would something like liftover not be recommended? honest question

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I think that is an alternative to a synteny analysis, but I only know liftover in terms of annotations. OP asks for "coordinates between these two strains", which I took to mean more than just genes or other similar features that would be included in a liftover. Maybe I misunderstood what they were after and synteny is overkill.

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