A splice site is the border between an exon and intron in a gene. These sites contain a particular sequence motif, which is necessary for recognition and processing by the RNA splicing machinery.
The S&S algorithm uses sliding windows of eight nucleotides, corresponding to the length of the splice site sequence motif, to identify these conserved sequences and thus potential splice sites. Using a weighted table of nucleotide frequencies, the S&S algorithm outputs a consensus-based percentage for the possibility of the window containing a splice site.
The S&S algorithm serves as the basis of other software tools, such as Human Splicing Finder, Splice-site Analyzer Tool, dbass (Ensembl), Alamut, and SROOGLE.