Outputs / Results


Spliceman takes either a set of genomic variants or DNA sequences with point mutations and compute how likely these single nucleotide variants alter splicing products. Read Methods and Interpretations for the computational algorithms this tool uses to generate the predictions.

The following explains what each field in the output page means:


Point mutation

When a sequence with one point mutation is provided, Spliceman needs at least an 11-mer with point mutation (or simply 11-mer) to kickstart its computation. Therefore this tool requires at least 5 flanking nucleotides on each side of the point mutation for each FASTA record.

The 11-mer used during the computation is reported in this field.


Wildtype (wt), Mutation (mt) and L1 distance

The mutation analysis fragments an 11-mer into a set of overlapping singly shifted hexamers. A point mutation alters six hexamers to new hexamers with new L1 distances. For instance, an 11-mer "acgta(a/c)gtagt" results in the 6 following comparisons as illustrated in the figure below.



We report the comparison that results in the highest L1 distance. Both the wildtype and mutant hexamers and their associated L1 distances are reported in these fields.


Ranking

For each 11-mer with a point mutation, the tool converts the highest L1 distance into a percentile rank. This rank is simply the percentage of how many times the highest L1 distance of an 11-mer is higher than all possible 11-mers with a point mutation. The higher the percentile rank, the more likely the point mutation is to disrupt splicing.