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What is Ginzu?

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What is Ginzu?

    Ginzu is a protocol that attempts to determine the regions of a protein chain that will fold into globular units, called "domains". It scans the protein chain sequence with successively less confident methods of detection to determine any homologs with experimentally determined structures, starting with PDB-BLAST, and followed by the more remote fold-detection method HHSEARCH. After any homologs are identified, a search of remaining regions is done with HMMER against the Pfam-A protein family database. Lastly, the PSI-BLAST multiple sequence alignment is used to assign regions of increased likelihood of possessing a contiguous domain based on sequence clusters. The final step consists of selecting cut-points between the domains (and possibly defining new domains based on the strongest cutpoints for any remaining long stretches of the sequence that have not already matched a homolog with a structure or Pfam-A) using the PSI-BLAST MSA.

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