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found non conserved regions between 2 genomes

Hey guys.

I'm wondering if have a tool that identifies non-conserved regions between 2 eukaryotic genomes (like pan-genomic tools for prokaryotes, that are capable of identify accessory genes).

genome blast alignment
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updated by harish harish • written by flogin flogin

At the simplest level, you could do local alignments between 2 genomes with something like mummer, find all the conserved regions, then simply flip all the coordinates you got back to find all the regions which were less conserved than that threshold.

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written by Joe Joe

2 answers

Hi I used to use the ECR browser for this type of question, you can find the details at https://ecrbase.dcode.org/. Just be aware that it was last updated in 2008! But this might be useful to you.

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written by Ian Ian

I'm gonna read about, thanks

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written by flogin flogin

Why not use Orthofinder? Give a couple of files containing protein sequences for each species and let it work its magic through.

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written by harish harish

I'm gonna read about, thanks

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written by flogin flogin

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