Lab Journal - Task 4 (PAH)

Evaluate sequence alignments

The perl script hhmakemodel can be found in /usr/share/hhsuite/scripts. It needs a input file in form of a result file from hhsearch with hit list and alignments (-i).

-d   <pdbdirs>         directories containing the pdb files (for PDB, SCOP, or DALI
                       sequences) (default=/cluster/databases/pdb/all)
-m   <int> [<int> ...] pick hits with specified indices  (default='-m 1')
-ts  <file.pdb>        write the PDB-formatted models based on *pairwise*
                       alignments into file.pdb

So first a hhr file is crated with the FASTA file of our protein PAH and the pdb database. The output file is called hhsearch_PAH.hhr. Furthermore we set the maximal reported lines in summary and alignments to 10000:
hhsearch -i /mnt/home/student/waldraffs/Masterpraktikum/PAH.fasta -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o hhsearch_PAH.hhr -Z 10000 -B 10000