Gene Cloning

224 Gene Cloning
well as the statistical test. The example used in the alignment in Figure 8.11
is explained in the next section and you will be able to see that the alignment
fits very well with what is known about the two proteins.
8.8 What Can Alignments Tell Us About the Biology of the
Sequences Being Compared?
Pair-wise comparison of two related sequences can be a very powerful tool.
The following example illustrates the sort of information that can be
deduced from this type of comparison. It involves the comparison of a protein
from different strains of a human adenovirus. Some types of this virus
are oncogenic, capable of causing tumors to develop, while others are not.
The protein E1A is the product of the virus “early region” and has been
shown to be involved in the induction of tumors. The dot-plot in Figure 8.8
and the alignment in Figure 8.11 show a comparison of the amino acid
sequences of the E1A protein from an oncogenic strain (12) with that of a
non-oncogenic strain (05). The strong diagonal line on the dot-plot (Figure
8.8) indicates that these sequences are very similar along large parts of their
length, which is to be expected since they are variations of the same protein;
you can see these regions of similarity on the alignment (Figure 8.11).
There are two large gaps which have to be introduced into the alignment,
marked with arrows in Figure 8.8. It is the extra sequence, starting at position
123 in the A1E12, which is not present in the non-oncogenic strain
which is responsible for this virus causing tumors. This observation from
sequence alignments has been tested in the laboratory by cloning this extra
sequence into the non-oncogenic strain and observing that it is then capable
of causing tumors in mice.
8.9 Similarity Searches
Imagine that you could do a pair-wise alignment with your query sequence
and every known sequence and then look at, say, the best 50 alignments.
This would tell you which of the proteins, for which sequence data was
available, were most similar to your query. If the structures and functions
of these proteins are known then they will give clues as to the structure and
function of your query sequence. DNA and protein sequence data are
stored in large publicly available databases (Box 8.2); in addition to the
sequence data these databases contain varying amounts of annotation. For
example, a typical entry in the protein database, SwissProt, gives a brief
description of the protein and its origin, references to papers describing
the derivation and analysis of the sequence, a comments section which will
identify any key features of the protein such as its activity and whether it
belongs to a characterized family of proteins, hyperlinks to relevant entries
in other databases and an outline of the key features of the sequence.
Hence searching this type of database provides access to an immense
amount of information.