PIntron

PIntron is a novel pipeline for computational gene-structure prediction based on spliced alignment of expressed sequences (ESTs and mRNAs).

PIntron is composed by four steps: Firstly, alternative alignments of expressed sequences to a reference genomic sequence are implicitly computed and represented in a graph (called embedding graph) by a novel fast spliced alignment procedure. Secondly, biologically meaningful alignments are extracted. Then, a consensus gene structure induced by the previously computed alignments is determined based on a parsimony principle. Finally, the resulting introns are reconciliated and classified according to general biological criteria.

A detailed description of the pipeline is available here.

Downloads

The latest stable version of PIntron is v1.2.0 (June 21, 2011).

PIntron is distributed as source code and as pre-built binary packages for some common platforms.

The latest source code version can be downloaded from the GitHub page as a zip or as tar.gz archive. It is also possible to clone the source repository using the following command:

  $ git clone git://github.com/AlgoLab/PIntron.git

The latest pre-built binary packages are available for the following platforms and architectures:

Older binary releases are available at this website while the corresponding sources are available at GitHub.

 Citation

The canonical publication of this software is:
… ICCABS

Documentation

Please refer to this page for the installation instructions and this page for the user manual.

License

PIntron is distributed under the terms of the GNU Affero General Public License (AGPL), either version 3 of the License, or (at your option) any later version.

PIntron is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

A copy of the GNU Affero General Public License is distributed along with PIntron and it is also available at the GNU website.

Contacts

For additional information, please contact Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, or Raffaella Rizzi.