Figure 1

Representation of start and stop codons in the splicing graph. Rectangles: exons. Angle lines: introns. Circles: stop codons. Arrows: start codons. Filled arows: start codons generated by alignment with proteins. Crossed arrows: start codons in-frame with an upstream acceptor site or a start codon. The following situations are considered and marked on the scheme:. (1) In each exon, for each possible reading frame, a stop codon closing this reading frame generates a stop-vertex. (2) If an exon contains a start codon preceded by a stop codon in the same reading frame, a start-vertex is generated. If a start codon coincides with the beginning of a protein-genome alignment, it generates a start-vertex irrespective of upstream stop codons (gray exon). In the latter case, no additional filters are applied (see the text). (3) Any start-vertex that is in-frame with an upstream acceptor site or a start codon is removed (crossed arrow).