blastx to compute complete, partial or missing genes

Question

[Mbillah]

I have a protein sequence and a chromosome. Now I want to find out how many complete, partial or missing genes in my chromosome by the blast. So that I used blastx program, Now how can I determine complete, partial or missing genes from the blast output.

Answer 1

[lieven.sterck]

In this case you're likely better of with doing a TblastX TblastN (so, blast your proteins(s) to your genome), this will make the post-processing a bit more straightforward. From the output you can then check if the complete protein sequence has been matched or not.

An alternative would be to run something like BUSCO (which will give you the complete/fragemented/... fraction of a core set of genes, as a kind of proxy for all proteins)

EDIT: should be tblastN in stead of tblastX , my bad.