Question: found non conserved regions between 2 genomes
0
gravatar for flogin
11 months ago by
flogin250
Brazil
flogin250 wrote:

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).

blast alignment genome • 275 views
ADD COMMENTlink modified 11 months ago by harish320 • written 11 months ago by flogin250

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.

ADD REPLYlink written 11 months ago by Joe18k
2
gravatar for Ian
11 months ago by
Ian5.7k
University of Manchester, UK
Ian5.7k wrote:

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.

ADD COMMENTlink written 11 months ago by Ian5.7k

I'm gonna read about, thanks

ADD REPLYlink written 11 months ago by flogin250
1
gravatar for harish
11 months ago by
harish320
harish320 wrote:

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

ADD COMMENTlink written 11 months ago by harish320

I'm gonna read about, thanks

ADD REPLYlink written 11 months ago by flogin250
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