Chapter 17

Genomics

We start with a couple of definitions: The genome is the ensemble of genes in an

organism, and genomics is the study of the genome. The major goal of genomics is

to determine the function of each gene in the genome (i.e., to annotate the sequence).

This is sometimes expressly designated as functional genomics. Figure 17.1 gives

an outline of the topic. The starting point is the gene; we shall not deal with gene

mapping, since it is already well covered in genetics textbooks. We shall view the

primary experimental data of genomics as the actual nucleotide sequence and reit-

erate that genomics could simply be viewed as the study of the nonrandomness

of DNA sequences. More comprehensively, genomics is the study of the structure,

function, and evolution of genomes, involving the sequencing and analysis of an

organism’s entire genetic material in order to gain insights into its development and

phenotype. Genomics has revolutionized biology, promising a deeper understanding

of the complexities of life and with potential applications to personalized medicine

(Chap. 26).

The first section of this chapter will briefly review experimental DNA sequencing.

The next essential step is to identify the genes. Initially, this was the sole or main

preoccupation, but since then it is recognized that promoter and other sequences

(including those generating small interfering RNA) possibly involved in regulation

must also be considered—in brief, all biochemically active sites—since understand-

ing of even a minimal phenotype must encompass the regulatory network controlling

expression and activity, as well as the expressible genes themselves.

Once the coding sequences (i.e., the genes) have been identified, in principle one

can determine the basic protein structure from the sequence alone (cf. Sect. 15.5.2).

Once the structure is available, the function might be deduced; there is no general

algorithm for doing so, but comparison with proteins of known function whose

structure is already known may help to elucidate the function of new genes. It might

not even be necessary to pass by the intermediate step of the structure in order to

deduce the function of a gene or at least to be able to make a good guess about it;

merely comparing sequences of an unknown function with the sequences of a known

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J. Ramsden, Bioinformatics, Computational Biology,

https://doi.org/10.1007/978-3-030-45607-8_17

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