Preface

Summary

The idea behind this book developed in late 2004–early 2005 while I was working on two unrelated projects in computational genomics. The first project involved the computational detection of small nucleolar RNAs (snoRNAs) in genome sequences. In the course of this work, I noticed – as others had, as well – that, in mammals, snoRNA genes are located within introns of protein-coding genes (so-called snoRNA host genes), which are often genes that code for ribosomal proteins. This observation led to speculation as to whether therewere additionalcommonfeatures of the introns and genes that contain snoRNAs. For example, are the host genes of homologous mammalian snoRNAs themselves homologous? Do those host genes have other shared functions beyond the fact that several of them code for ribosomal proteins? Are the introns that contain the snoRNAs consistently longer (or shorter) than the average introns found in these genes? Are the snoRNAs found at any characteristic distance from the nearest exon-intron junctions in their host gene? To answer these questions would require accessing sequence and annotation data for both the human and mouse genomes and performing some simple calculations and statistics on that data. Moreover, because therewere some200humansnoRNAs already known(and a similar number of mouse snoRNAs), performing this data acquisition and manipulation would require computer processing.