Alternative splicing prediction
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There are plenty of bioinformatic tools out there that predict alternative splicing events from RNAseq (or other data, I'm not sure). (http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=4680). You look through the tools listed in the link to find a tool that suits your need.
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Do you mean predict on the basis of gene sequence which of its exons are constitutively spliced vs which ones are alternatively spliced?
yeah prediction on the basis of gene sequence.
I see some tools online such as ASSP, AVISPA, HSF. Have you tried any of these? Do they work for your kind of analysis?
I want to develop my own. So how can i beat them..could you have any idea...
Do you mean what they are lacking? I don't know for sure. For any tool, you can either increase the efficiency or add more features to it. You can collaborate with a biologist and compare all these tools for their efficiency if no one has done it so far. May be that will give a clue.
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