Finding Out Homologs Of A Protein
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.
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Last time I was in a seminar by Sean Eddy, he said jackhmmer was the recommended tool for your problem.
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