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support:hpc:software:pispred

PSIPRED Protein Structure Prediction

Prerequisites

Below is a list of prerequisites for using PSIPRED:

To load PSIPRED type the following:

$ module load gcc blast psipred

PSIPRED requires PSI-BLAST and Impala software from the NCBI toolkit, and also install appropriate sequence data banks. The uniref90 protein dataset is recommended as a suitably large and “complete” set of proteins. These paths are hard coded into /share/apps/psipred-3.21/runpsipred.

Example Usage

The software is located at /share/apps/psipred-3.21. The runpsipred is the script to use to run the software.

To use PSIPRED with BLAST+, use /share/apps/psipred-3.21/BLAST+/runpsipredplus (and check out the README in the same directory).

Example Usage

Example Run

module load gcc blast psipred hhsuite
cp /share/apps/psipred-3.21/example.fasta .
pfilt example.fasta > examplefilt
formatdb -t example.file -i examplefilt
runpsipred example.fasta

Running PSI-BLAST with sequence example.fasta …
Predicting secondary structure…
Pass1 …
Pass2 …
Cleaning up …
Final output files: example.ss2 example.horiz
Finished.

farm:~> more example.horiz

  # PSIPRED HFORMAT (PSIPRED V3.2)

  Conf: 939999865663389999999999985799148840899995786788987999825779
  Pred: CCEEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCEEEEEECCCC
  AA: PKALIVYGSTTGNTEYTAETIARQLANAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWG
              10        20        30        40        50        60


  Conf: 999998889288888710599999759999316997478989999999999847994624
  Pred: CCCCCCCCCHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEECC
  AA: DDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSYEYFCGAVDAIEEKLKNLGAEIVQ
              70        80        90       100       110       120


  Conf: 632430899999210887999998629
  Pred: CCEEECCCCCCCCCHHHHHHHHHHHHC
  AA: DGLRIDGDPRAARDDIVGWAHDVRGAI
             130       140
    
support/hpc/software/pispred.txt · Last modified: 2012/02/01 15:12 by tlknight