Alternative Splice Site Predictor (ASSP)

Splice site prediction

ASSP predicts putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons. Skipped splice sites are not differentiated from constitutive sites. Non-canonical splice sites are not detected. Alternative splicing is predicted based on the DNA/RNA sequence information only. For splice site prediction within a sequence putative splice sites are preprocessed using position specific score matrices. By increasing the cutoff level of these matrices you may prevent false splice sites to be detected as putative alternative isoform or cryptic sites. However, high stringency matrices (high cutoff) will not detect weak alternative isoform or cryptic splice sites. For further information refer to section evaluation.

Reference:

Wang M. and Marín A. 2006. Characterization and Prediction of Alternative Splice Sites. Gene 366: 219-227.

To analyse multiple sequences please use ASSP MultiSEQ. ASSP MultiSEQ produces an output file in text format, which can be parsed easily for automation.

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