Background and Motivation. Acquiring knowledge of a gene is central in interpretation of what it does. A gene is close to the “the atom ” of molecular biology (Keller, 2002) and must be annotated in terms of structure, selection profile, constraints, regulatory signals and its relation to other genes. In its extreme form, this necessitates understanding of the complete organism as a gene is part of a large interacting network of genes and signals. So making restrictions of this problem to define a worthwhile and still challenging problem is necessary. This project focuses on the identification and the characterisation of regulatory elements, which is likely to be a major challenge for quite some time to come and this project would easily scale to a complete PhD. However, it is also possible to formulate a pilot version, that is of interest in itself. This is a cartoon of a standard gene. The red segments are exons, whose combined length must be a multiplum of 3. The region between exons are called introns. Regulatory signal are shown in blue. Homologous variants of this gene is then observed in many species. Signals are often found by comparison and observing that they evolve slower than surrounding regions. It is still a significant challenge to recognise and categorise the wide range of cis-acting regulatory elements by computational analysis alone (e.g. promoters, enhancers, locus control regions, boundary elements and silencers) that control gene expression (Maston et al., 2006). A ladder of ambition. The purpose of this section is both to state what is possible and what isn’t. 1. Finding slowly evolving segments as indicator of regulatory signals. Homologous analysis has recently become more powerfu
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