12.7 Predator - Secondary Structure Prediction
This plug-in interfaces VEGA ZZ to Predator* that allows
to predict the secondary structure of a protein starting from the 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
that can contains on or more sequences according to Predator method (in FASTA, CLUSTAL,
MSF formats) and the file name of the custom database.
Checking the Sequence ID box, you can select the sequences that Predator uses as
query. The default sequence is the first in the sequences file.
The 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
the Files box.
In the 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 the Run button, the calculation begin and can be stopped clicking on the Abort button. The output is directly captured in the big edit box and it's shown like 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 on the Help label, the document is shown, and clicking on About
label, the following copyright dialog appears:
For more information about Predator test, see the original documentation in the VEGA\Predator\Docs directory.
*Predator is copyrighted by Dmitrij Frishman & Patrick Argos