Fig. 3.
Example of hidden states representing three different transcripts. Five exon start sites and four exon end sites divide the gene into eight segments. Note, however, that the TSS bounding X1 from the left and the TES bounding X8 from the right are not labeled here since our model treats them differently (see main text). Therefore, Ms = 4, Me = 3 and M = 8. The three sequences of states of Z, (1, 1, 0, 1, 0, 0, 1,1), (0, 1, 0, 0, 0, 1, 1,1) and (1, 1, 0, 0, 0, 0, 1,0), represent the three transcripts t1, t2 and t3, respectively