Today we shall examine de Bruijn graphs for two structures that occur frequently in genomes or transcriptomes. The reason for studying them together will be apparent by the end of this post.
Let us first construct a graph for two alternatively spliced transcripts A and B for a gene. The regions shown in yellow and red are transcribed in both isoforms, whereas the green region is present only in A.
The de Bruijn graph is shown in circle and arrow format, and the paths for two transcripts are marked by dotted lines. We shall explain the graph construction qualitatively instead of going into nucleotide level detail. We recommend you to pick your favorite gene and do the detailed construction yourself by following rules explained earlier.
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