Using Pred2ary
From the buttons at the bottom of the screen, you can:
- Load or Save proteins to a file (click here for information on
protein formats).
- Automatically get multiple sequences for a protein using the
local or online BLAST servers.
- Predict the secondary structure and
structural class of your proteins.
- Print the current prediction to the printer. This will automatically
wrap lines if the font is set too large.
There is a known bug with printing on
some systems.
- Choose a sequence from a profile of
sequences to focus on.
- Quit the program.
Other things you might do from the main screen are:
- Select which jury to use - under the
"Jury" menu.
- Get to the Log
window: click on the "Log" tab just above the main window.
- Change the font size, under the "Font" menu.
The other options are pretty self explanatory:
- wrap lines - wraps the display of the protein after every N amino acids.
(you can select this number)
- graph prediction - if a prediction of secondary structure has been
made, this box toggles graphing of predicted secondary structure
probabilities below the sequence(s) and predictions.
- show profile - this shows all sequences in a profile, if you
have multiple sequences loaded.
- show single - this shows only a single sequence instead of
the whole profile, if you have multiple sequences loaded. The
sequence shown will be the consensus sequence if you loaded from
a MSF file; otherwise, it will be the chosen or BLAST'ed sequence.
Pred2ary can be run interactively or non-interactively. Here is
a description of command line options
for non-interactive use.
Before using Pred2ary, please read the
license and
register the program.
If something isn't working, please check the
known problems,
and submit a bug report if something isn't working.
Here are references for Pred2ary.