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sokrypton / GREMLIN

GREMLIN is a method to learn a statistical model of a protein family that captures both conservation and co-evolution patterns in the family. The strength of measured co-evolution is strongly predictive of residue-residue contacts in the 3D structure of the protein.
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How to generate input MSA file #1

Open CryoSky opened 5 years ago

CryoSky commented 5 years ago

Hello, I want to generate the input MSA file through hhblits. However, I found the output fasta file include lots of gaps like below: -------------------------------------------------------------------------------------------------------------------------------------------------------T-----------------------------E----------------------R-----------------------Q-------------------------------I----------A-------H--I--------------------------IS-------------------T---M------------------------------------------------D---------------II---T------N------------------------------------------------H-T Although my query sequence has only 137 residues, the output fasta file give me 3098 residues for each sequence if you load this file to GREMLIN. It's because hhblits aligned all founded sequence, I want to know do you have a code to align founded sequence to the first sequence (or your query sequence) in fasta?

CryoSky commented 5 years ago

Or could you share the command of hh-suite you use to prepare input files for GREMLIN? Many thanks!