PPfold

LAST UPDATE: Apr 18, 2011 (publications updated)

PPfold is a new version of pfold, written in Java 5.0. It can predict the consensus secondary structure of RNA alignments through a stochastic context-free grammar coupled to an evolutionary model.

PPfold is multithreaded, and can solve the structure of much longer alignments than pfold without breaking down (due to underflow errors). It is also platform-independent and much more user-friendly than pfold. PPfold can be downloaded as a standalone program as well as a free plugin to the CLC Workbenches. (Scroll down for downloads!)

NEW RELEASE (Feb 16): PPfold version 2.0 includes maximum likelihood tree estimation. Download the newest version below.

PLEASE NOTE that while stable and well-tested, the PPfold package does not yet include the following functions of the pfold webserver:

Stem extension (can be done using a C program you can download below)
Incorporation of constraints
Export of dotplots in .ps format (can be done using a C program you can download below)

We are working on including these and additional functionalities in PPfold, and creating a webserver for it.

PPfold has been created as part of the Collaborative Minigrid Project, in close cooperation between

If you experience any issues, or have questions or comments, email:

Zsuzsanna Sukosd (zs@mb.au.dk)

Instructions and download links

PPfold (standalone)

Choose this if you just want to run the program with no (or very rudimentary) user interface

Version 2.0 (current release): PPfold-v2-0.jar

(Old versions below.)

Given that you have Java installed on your computer, you can execute it

From the desktop: Simply double-click the file. It should pop up with a file chooser dialog. Select the input alignment (it must be in FASTA format). PPfold will then run using all the processors of your computer, and it will save the results into the same folder as the alignment file. Make sure you have write permissions to that folder! You can visualize the output files using many programs.
From the command line: type "java -jar PPfold --help" for information on command-line arguments and options.

To try it out with an example, download:

gca-alignment.fasta

The parameter file used in PPfold can be downloaded here (useful in case you want to use a different one and need the format):

matrices.in

PPfold (CLC plugin)

Choose this if you want to integrate it into a CLC Workbench:

Version 2.01, compatible with CLC Workbench versions 6.x (download link from CLC bio): PPfold.cpa

(Old versions below.) Instructions on how to use it can be found here: USING IT.

PPfold (source code, old versions and extras)

Choose this if you want to have a look at the source code, need the extra programs or want to use the old versions:

Only PPfold	PPfold.zip
PPfold + CLC plugin integration	PPfold-plugin.zip
PPfold + CLC plugin integration + minigrid integration	PPfold-minigrid-plugin.zip (not yet available)
Extra C programs (from pfold)	pfold-extras.zip
PPfold version 1.0 binary (no longer maintained)	PPfold.jar
PPfold plugin version 1.0, CLC Workbench versions 5.x (no longer maintained)	PPfold.cpa

Changelog

Current release: Version 2.0/2.01.

New features include maximum likelihood tree estimation, small bugfixes and a better user interface. Note changed command-line options (more UNIX-like than version 1.0)
Version 1.0. First release

Publications

Z. Sukosd, B. Knudsen, M. Vaerum, J. Kjems, E.S.Andersen. Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars BMC Bioinformatics 12:103, 2011