Graph Theory and Networks in Biology by Oliver Mason and Mark Verwoerd http://www.hamilton.ie/systemsbiology/files/2006/graph_theory_and_networks_in_biology.pdf
Efficient Systems Biology Algorithms for Biological Networks over Multiple Time-Scales: From Evolutionary to Regulatory Time
http://cs.nyu.edu/mishra/PEOPLE/mitrofanova_antonina.pdf
Hi Tayyiba,
Sorry, you did not explain you question well. I guess your are looking for Alternative splicing and functional prediction analysis tool/script.
You can use "AltAnalyze" which is a freely available, open-source and cross-platform...