Alternative splicing visualization tool...
ASIP Work Flow
We identify and visualize alternative splicing events in the following three steps:
- Align all cDNA/EST sequences against their genome using spliced-alignment program GeneSeqer. A typical alignment was shown in the following figure:
- Process the GeneSeqer alignments, extract exon/intron information and compare their coordinates to find overlapping introns/introns and introns/exons. Then we classify these overlapping events into different AS type. This process was carried out by a pipeline named ASpipe. To ensure quality, only reliable introns and exons were considered in this step.
- To publicize and visualize the data, we wrote an HTML interface and used CGI script to access the database (SpTAG). Perl module GD.pm was used to generate pictures. AS events were specifically highlighted, as shown in the following figure. A standalone version of these scripts will be available soon (ASviewer)