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biocore / microprot

structural annotation pipeline for microbial genomes and metagenomes
BSD 3-Clause "New" or "Revised" License
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PDB match: search #2

Closed tkosciol closed 7 years ago

tkosciol commented 7 years ago

Use pHMMer (from HMMer /projects/microprot/tools/HMMer/) or HHsearch (from HH-suite) to search an amino acid sequence for hits against the PDB database.
suggested parameters for phmmer: -E 0.001 --domtblout

make sure the script is able to process multiple hits to different PDBs, i.e. gene has several domains, each of them matching to a different PDB structure.

tkosciol commented 7 years ago

added as PDB_match rule in Snakemake