A survey of tools for variant analysis of next-generation genome sequencing data http://bib.oxfordjournals.org/content/early/2013/01/21/bib.bbs086.full
Hi Andaleeb,
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If you are looking for any online tool then try Alternative Splice Site Predictor (ASSP) which predicts putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons....