12.13 Predator - Secondary Structure Prediction

This plug-in interfaces VEGA ZZ to Predator* that allows to predict the secondary structure of a protein starting from their primary structure. It takes as input a single protein sequence to be predicted and can optimally use a set of unaligned sequences as additional information to predict the query sequence. The mean prediction accuracy of PREDATOR is 68% for a single sequence and 75% for a set of related sequences.
To open the main window, you must select Bioinformatics Predator from the main menu.

In Files box,  you can enter the file  containing on or more sequences according to Predator's supported files (in FASTA, CLUSTAL, MSF formats) and the file name of the custom database.
Checking Sequence ID box, you can select the sequences that Predator uses as query. The default sequence is the first in the sequences file. Database box allows to select the database used to predict the secondary structure. If Custom is selected, you can insert the custom database file name in Files box. In Options box, you can change some Predator parameters:

• Single sequence: the algorithm uses only one sequence for the prediction (less accurate).
• All sequences: the secondary structure in predicted of all sequences.
• Long output: Predator shows more information.
• Show progress: show the calculation progress.

Pressing Run button, the calculation starts and can be stopped clicking on Abort button. The output is directly captured in the big edit box and it's shown as below:

 Info>  3fis.brk   : .................................................!
 Info>  FIS_HAEIN  : .................................................!
 Info>  NTRC_AZOBR : .................................................!
 Info>  NTRC_RHIME : .................................................!
 Info>  NTRC_BRASR : .................................................!
 Info>  NTRC_RHOCA : .................................................!
 Info>  ATOC_ECOLI : .................................................!
 Info>  NTRC_KLEPN : .................................................!
 Info>  FLBD_CAUCR : .................................................!
 Info>  NTRC_ECOLI : .................................................!
 Info>  NTRC_SALTY : .................................................!
 Info>  NTRC_PROVU : .................................................!
 Info>  Identical 7-residue fragments found in:
 Info>  3fis.brk B

> 3fis.brk
              .         .         .         .         .
1    PLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQT   50
     _HHHHHHHHHHHHHH_________HHHHHHHHHHHHHHHHHHHH____HH

              .         .   
51   RAALMMGINRGTLRKKLKKYGMN                              73
     HHHHHH___HHHHHHHHHH____

Clicking Help label, this document is shown, and clicking About label, the following copyright dialog appears:

For more information about Predator software, see the original documentation:

• Release notes (relnotes.txt).
• How to run the command line version (how2run.txt).
• Predator manual (predator.txt).

*Predator is copyrighted by Dmitrij Frishman & Patrick Argos