Input Instructions:

Please upload a file with one variant per row. For each variant, you need to include the following with tab deliminaters:

VARIANT_NAME	WILDTYPE_SEQ	VARIANT_SEQ	WILDTYPE_PSI

VARIANT_NAME is a user chosen id for the event
WILDTYPE_SEQ is the sequence of the whole wildtype alternative exon and 6 nucleotides of the downstream intron (i.e. GGT…CAG|gtaagt).
VARIANT_PSI is the alternative exon sequence including variants.
WILDTYPE_PSI is the percent spliced in (PSI) fraction for the wildtype sequence--i.e. the percentage of alternative exon inclusion. This should be between 0-100.
Variants are not limited to SNPs. Variants can be included anywhere in the alternative exon, as well as in the splice donor. As of now, we do not support intronic variants (other than in the alternative exon's splice donor), but we hope to in the future. For now, we recommend scoring intronic variants with SPANR.

Output File:

The output file will download automatically. It will contain the predicted PSI for the variant sequence as well as the change in PSI (delta PSI) in tab deliminated format.

variant_1	GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGAgtaagt	GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCAATTAAGGAgtaagt	21
variant_2	GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGAgtaagt	GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTGAATTAAGGAgtaagt	21
variant_3	GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGAgtaagt	GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAACTTAAGGAgtaagt	21
variant_4	GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATTAAGGAgtaagt	GGTTTTAGACAAAATCAAAAAGAAGGAAGGTGCTCACATTCCTTAAATGAAGGAgtaagt	21