Figure 2.

Criteria of merging. There are three basic forms of compatibility between two ESTs. In case 1, they have a consecutive overlap of internal splice-sites and no other splice-site that overlaps the genomic extent of the other EST. In case 2, we allow some mismatch of length ≤m at the exon boundaries. In case 3, we allow bridging over tiny introns of size ≤n. Thresholds m and n can be modified. In the ClusterMerge algorithm the comparison can be parameterized as a combination of these three basic cases.