Predict Alt. 5' Splicing Variants
Input Instructions:
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. Please include both splice donors and all the
sequence between them (i.e. CAG|GTAAGT…GAG|gtaagt)VARIANT_PSI
is the alternative exon sequence including
variants. Variants can be included in the splice donors as well as
between them.WILDTYPE_PSI
is the percent spliced in (PSI) fraction
for the wildtype sequence--i.e. the percentage of splicing at the
downstream splice donor. It should be between 0-100.As of now we do not support variants that are exonic or intronic to both the splice donors, but we hope to in the future. However, in our paper, we find that variants between alternative splice donors are much more likely to alter splicing than those upstream or downstream of both splice donors.
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.Example (CDC45):
Below is an example file. To get the output for this example file, just press submit. To score your own variants, upload your own file, and then press submit.var_1 GAGGTGGTCCAGAGCCAGgtgacg GAGGTGGTCCTGAGCCAGgtgacg 87 var_2 GAGGTGGTCCAGAGCCAGgtgacg GAGGTGGTCCATAGCCAGgtgacg 87 var_3 GAGGTGGTCCAGAGCCAGgtgacg GAGGTGGTCCAGTGCCAGgtgacg 87 var_4 GAGGTGGTCCAGAGCCAGgtgacg GAGGTGGTCCAGAAGCCAGgtgacg 87