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.
Wang M. and Marín A. 2006.
Characterization and Prediction of Alternative Splice Sites. Gene
To analyse multiple sequences please use ASSP MultiSEQ. ASSP MultiSEQ produces an output file in text format, which can be parsed easily for automation.