Abstract
Genome sequencing efforts of the last decade have produced a large amount of data, which has enabled whole-genome comparative analyses in order to locate potentially functional elements and study the overall patterns of phylogenetic conservation. In this paper we present a statistically based method for the characterization of these patterns in mammalian DNA sequences. We have applied this approach to the study of exceptionally well conserved homeobox gene clusters (Hox), based on an alignment of six species, and we have constructed a map of Hox cataloguing the conserved fragments, along with their locations in relation to the genes and other landmarks, sometimes showing unexpected layouts.
Highlights
The power of comparative analysis of genomic sequence data has been recognized for many years
As soon as significant amounts of mammalian genomic sequences became available, including homeobox gene clusters (Hox), researchers started looking at large-scale synteny and other comparative features
Due to the deactivation of three genes between HoxB13 and HoxB9 this left us with a large intergenic region at the opening end, which was beneficial for our study (Figure 2)
Summary
The power of comparative analysis of genomic sequence data has been recognized for many years. It is generally understood that conserved regions did not succumb to the evolutionary drift due to the effect of deleterious mutations, and sequence alignments became important for locating functional loci in DNA (Miller et al, 2004). For larger regions, such as gene exons, even pairwise alignments are already sufficient if the target species are chosen well, but for the detection of subtler signals one needs multiple sequences. Projects directed towards targeted sequencing of genomic regions for the purpose of the analysis of conservation (Thomas et al, 2003; The ENCODE Project Consortium, 2004; Margulies et al, 2005) have already produced substantial results (The ENCODE Project Consortium, 2007; King et al, 2007)
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