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3 months ago
jet
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0
I am currently building some models on DNA-binding residues. One of the features I am using involved HMM profiles of a protein sequence based on a protein database. Basically, a few previous papers involved getting the HMM profiles for a protein sequence as an input, using HHblits, so that was what I did as well.
This is my input:
hhblits -i temp.fasta -d databases/scop70_1.75 -ohhm out.hhm
However, I am notice something strange with my output. There are alot of seemingly "useless" rows.
The image above shows the output from a input sequence that is quite long, around ~600. This keeps repeating until the 300th-400th residue.
May I know what is causing this, and will this be an issue?
