Figure 3.

Extension versus nonextension. According to the evidence, splice-site 2 only appears together with splice-site 1. According to our logic of merging, sequence x can only merge with sequences that at least have splice-site 1 or 2, with the rest of the splice-sites either compatible or non-overlapping. In this case x can merge with y but not with z. To include splice-site 2 in transcript z, we would have to find in the evidence an EST with at least splice-sites 3 and 2. Our method therefore produces a and b from the available evidence and not a′. Other methods referred to in the text would sometimes produce a′ and b instead, trying to extend the transcript as much as possible, but this does not agree with the evidence.