How can I find gene cluster containing certain gene?

Question

[kgwkk2]

I ran antiSMASH to get gene cluster data from WGS. But I couldn't find certain cluster that described on prior study. So I want to find gene cluster which contains certain protein sequence (from NCBI) by homology. I think blast program will make it, but blast each gene cluster one by one will take a lot of time. I can't figure out simple way to blast antiSMASH output data. Can you recommend any python code or program to make it simply?

[Ernest Bonat]

finding a gene cluster can be done by using k-means clustering machine learning algorithm. this clustering algorithm is the most popular in machine learning projects workflow today. in fact, i'm writing a blog paper about this topic now. i think, it will be published by the end of this month. let me know how can i help?

[Ram]

Are you writing a blog post about finding gene clusters in antiSMASH using machine learning or general clustering of genes using k-means? If it's the latter, you're spamming posts with irrelevant links. Please stop doing this or your account will be suspended. Like I said before, add a Blog type post instead.

[Ernest Bonat]

this post does not include any irrelevant blog paper links at all. thank you for letting me know.

Answer 1

[timothy.kirkwood]

Blast the gene against the whole WGS to get a location, then just find that location using the antiSMASH summary/output?