A novel pipeline for gene-structure prediction based on spliced alignment of transcript sequences (ESTs and mRNAs) against a genomic sequence.
Description
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 alignment 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.
Please cite the following paper when using PIntron:
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text, Computational Advances in Bio and Medical Sciences, IEEE International Conference on, pp. 33-39, 2011.
doi:10.1109/ICCABS.2011.5729935
Please refer to this page or to the README file in the source distribution for the detailed usage notes.
Download
The latest stable version of PIntron is v1.2.17 (Nov. 15, 2011).
PIntron is only distributed as source code.
The latest source code version can be downloaded from the GitHub page as a zip or as tar archive. It is also possible to clone the source repository using the following command:
git clone https://github.com/AlgoLab/PIntron.gitOlder versions are also available.
Install
Please refer to this page or to the INSTALL file in the source distribution for the detailed installation instructions.
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.
Authors
The joint main contributors of this project are Yuri Pirola (yuri.pirola@gmail.com) and Raffaella Rizzi (rizzi@disco.unimib.it).
The work has also greatly benefited from the contribution and the supervision of Paola Bonizzoni (bonizzoni@disco.unimib.it) and Gianluca Della Vedova.
To ask for information, please contact any of the authors.
