Biology Reference
In-Depth Information
Chapter 2
Comparative Genome Analysis
Robert M. Waterhouse, Evgenia V. Kriventseva
and Evgeny M. Zdobnov
1. Introduction
Comparative genomics takes advantage of whole-genome-scale sequen-
cing projects to develop strategies to interpret patterns of natural genome
sequence variations. It strives to understand the principles of molecular
evolution and recognize functional elements encoded in genomes. The
analyses rely on both intragenomic and cross-species comparisons to elu-
cidate and quantify the evolutionary processes acting on genomes and
how they may translate into functions and phenotypes. The large-scale
nature of genomic analyses, as well as the rapidly increasing number of
sequenced genomes, necessitates a computational approach to the man-
agement and interrogation of the data. Comparative genomics has
revealed a great deal about the repertoire of protein-coding genes, has
helped to mature our understanding of certain features such as alter-
native splicing of encoded proteins, regulation of gene expression, and
stability of genome architecture. Nevertheless, there often appear to be
even more questions raised than answered. For example, our under-
standing of the repertoires of non-protein-coding RNA genes or con-
served noncoding sequences remains generally more limited. In conjunction
with emerging functional genomics data generated through the interro-
gation of molecular functions at the genome scale, comparative genomics
goes beyond the level of describing trends in feature similarities and
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