To quantify the differences in splicing patterns between mRNAs or ESTs derived from a gene locus, a new measure called the splice junction difference ratio (SJD) was developed. For any pair of mRNAs/ESTs that align to overlapping portions of the same genomic locus, the SJD is defined as the proportion of splice junctions present in both transcripts that differ between them, including only those splice junctions that occur in regions of overlap between the transcripts (Figure 4). The SJD varies between zero and one, with a value of zero for any pair of transcripts that have identical splice junctions in the overlapping region (for example, transcripts 2 and 5 in Figure 4, or for two identical transcripts), and has a value of 1.0 for two transcripts whose splice junctions are completely different in the regions where they overlap (for example, transcripts 1 and 2 in Figure 4). For instance, transcripts 2 and 3 in Figure 4 differ in the 3' splice site used in the second intron, yielding an SJD value of 2/4 = 0.5, whereas transcripts 2 and 4
