Figure 1.

The figure illustrates two gene-factorizations into 7 and 4 pseudo-exons of the genomic sequence G. Let S₁, S₂ and S₃ be EST sequences in S agreeing to the genomic sequence G, where sequence S₁ = ABDEF, S₂ = ABCDE and S₃ = BDEFG, each letter in {A, B, C, D, E, F, G} denotes a sequence (A). In (B) and (C) two alternative EST-genome alignments of sequences S₁, S₂ and S₃ are represented: each EST factorization of S_i associated with the EST-genome alignment is shadowed. Pseudo-exons in the gene-factorization are colored white, while introns are in grey. Segments labelled by letters represent regions of the genomic sequence that align to a substring of the input sequence of the corresponding letter. Note that an approach that aligns independently each sequence S₁, S₂ and S₃ to G, one after the other, may produce the gene-factorization <A, B, C, D, F, E, G> consisting of 7 pseudo-exons (B), while the one minimizing the number of pseudo-exons provides only 4 pseudo-exons (C). Indeed, there are EST factorizations of each S_i that are compatible or variant compatible with the gene-factorization G_E = <AB, C, DE, FG>. More precisely, <AB, DE, F> is an EST-factorization of S₁ that is compatible to G_E. Then <AB, C, DE> is an EST-factorization of S₂ compatible to G_E. Finally, <B, DE, FG> is an EST-factorization of S₃ compatible with G_E (C).