An Investigation on Genomic Repeats

Motivated by a general interest to understand sequence based signaling in the cell, and in particular how (even distal) genomic strings communicate each other in the transcriptional process, we present a bioinformatic investigation on genomic repeats which occur in multiple genes. Unconventional graph based methods to abstractly represent genomes, gene networks, and genomic languages are provided. In particular, the distribution of long repeats along genomic sequences from three specific organisms (genome of N. equitans, of E. coli, and chromosome IV of S. cerevisiae) is computed, and efficiently visualized along the entire sequences, with the unexpected result to have most of them occurring inside genes.