250

17

Genomics

Fig. 17.1 The major parts of genomics and their interrelationships. The passage from sequence to

function can bypass structure via comparison with sequences of known structure

function, focusing on the sequence similarities, may be sufficient. The comparison

of sequences of gene coding for the same (functionally speaking) protein in different

species forms the basis for constructing molecular phylogenies, via their differences.

The huge collections of gene and protein data now available have encouraged the

so-called “hypothesis-free” or “minimalist” approach to sequence analysis. ¹ This is

discussed in Sect. 17.6. Possibly the greatest value of this approach is not so much

in elucidating particular phenomena such as a function of a specific gene, but rather

in approaching an answer to the broader question of the meaning of the genome

sequence, without the distraction of imposed categories such as “gene”, which may

be, as is currently all too apparent, very difficult to define unambiguously.

17.1

DNA Sequencing

The raw data used for genomic analysis are DNA sequences. This and the next section

briefly describe the major experimental approaches involved. For investigating the

RNA in the cell—the RNome, which has taken on a renewed importance since the

discovery of the so-called “noncoding” RNA (i.e., not ultimately translated into

protein)—the RNA would normally first have to be converted into complementary

DNA (cDNA).

1 It is sometimes said of this approach, rather disparagingly perhaps, that “one can apparently make

significant discoveries about a biological phenomenon without insight or intuition”. Possibly this

criticism derives from J. S. Mill’s view that deduction cannot produce new knowledge. At any rate,

it belies the fact that in reality once some unsuspected structural feature in the sequence has been

discovered purely by manipulating the symbols; a great deal of insight and intuition is generally

applied to make sense of it.