Alternative Splice Site Predictor

ASSP - Overview
Prediction of alternative splice sites
ASSP - Definitions
ASSP - Evaluation
Sequence analysis software

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.


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.

Enter your sequence (human):
(FASTA or raw sequence, DNA or RNA)

(include at least 70 bp before the first and after the last splice site)
Cutoff values:
False splice site cutoff for acceptor sites:
False splice site cutoff for donor sites:
Further information about cutoff values
Graphical output options:
Display stop codons
Display codon usage; windowsize (codons):
Codon usage is calculated from human codon frequencies  

For building your own models for searching for biological signals in DNA or RNA see the Seqool sequence analysis program package.

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Last Changes 10.01.2011