clustering sequences in two different assemblies to find similarities based on sequence

Question

[Mehmet]

Dear all,

I have two assembly, and I want to cluster of each sequence in two assemblies to find how similar the two assembly in terms of sequence. I used cd-hit-est-2d. I also want to use another tool for this. Any recommendation?

Thank you

[Buffo]

Nucmer or mummer is just what you are lookingfor (I think)

Answer 1

[renjukrishna13]

The other strategy I would recommed is to translate and get the peptides in all frames and do a protein level clustering. You could use latest tools like MMseq, https://github.com/soedinglab/MMseqs2 to do the clustering .