To quantify the difference in splicing patterns between mRNAs or ESTs derived from a gene locus, the splice junction difference ratio (SJD) was calculated. For any pair of mRNAs/ESTs that have been aligned to overlapping portions of a genomic locus, the SJD is defined as the fraction of the splice junctions that occur in overlapping portions of the two transcripts that differ in one or both splice sites. A sample calculation is given in Figure 4. The SJD measure was calculated by taking the ratio of the number of 'valid' splice junctions that differ between two sequences over the total number of splice junctions, when comparing a pair of ESTs across all splice junctions present in overlapping portions of the two transcripts. A splice junction was considered valid if: the 5' splice site and the 3' splice site satisfied either the GT..AG or the GC..AG dinucleotide sequences at exon-intron junctions; and if the splice junction was observed at least twice in different transcripts.
