PIntron is a tool for computing the exon/intron structure and the full-length isoforms of a genomic regions from a set of transcripts and the genomic sequence.
It computes the splicing alignments of the transcripts against the reference genome, it amalgamates the alignments to compute the exon-intron structure and then it computes the full-length isoforms.
PIntron is a command-line set of program that can be run on Linux 32/64 bit or Mac OS X. It is released under the open source AGPLv3 license.
The program (source code) and documentation can be found at www.algolab.eu/PIntron. To compile PIntron you need the usual GNU toolchain. To run it, you need Python and Perl.
Below is the the full-length isoforms computed on gene TP53.