Finding Out Homologs Of A Protein

Question

[Pappu]

I am trying to find out homologs of a protein in which the sequence similarity is very low among various species. So I made HMMs based on MSA of known protein sequences of the family to search for potential partners in the database using HMMER/HHSUITE.

I am wondering if there are any other machine learning (SVM) or other efficient techniques for doing this.

Answer 1

[14134125465346445]

Last time I was in a seminar by Sean Eddy, he said jackhmmer was the recommended tool for your problem.

[Pappu]

I am aware of jackhmmer. It is for searching a particular sequence against a database. However I want to search a MSA against a database.