Best 60 Determining Alternative Splice Sites

Determining Alternative Splice Sites Determining Alternative Splice Sites

Determining Alternative Splice Sites

How is alternative splicing predicted in 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.

How to prevent false splice sites from being detected?

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.

How are skipped splice sites differentiated from constitutive and non-canonical sites?

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.

What splice forms should be used to identify an alternative splice event?

Usually, a pair of splice forms that match exactly at one splice site (donor/acceptor splice site, i.e. 5′/3′SS) and differ at the other (3′/5′SS) is required to identify an alternative splice event ( 4 ).

Determining Alternative Splice Sites

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