Abstract:
A tandem repeat is a sequence of adjacent repetitions of a nucleotide patternsignature,
called its motif, in a DNA sequence. The repetitions may either
be exact or approximate copies of the motif. A minisatellite is a tandem
repeat whose motif is of moderate length.
One approach to searching for minisatellites assumes prior knowledge
about the motif. This approach limits the search for minisatellites to
specified motifs. An alternative approach tries to identify signatures autonomously
from within a DNA sequence. Several different algorithms that
use this approach have been developed. Since they do not use pre-specified
motifs, and since a degree of approximation is tolerated, there may be ambiguity
about where minisatellites start and end in a given DNA sequence.
Various experiments were conducted on four well-known software packages
to investigate this conjecture. The software packages were executed on
the same data and their respective output was compared. The study found
that the selected computer algorithms did not report the same outputs. The
lack of precise definitions of properties of such patterns may explain these
differences. The difference in definitions relate to the nature and extent of
approximation to be tolerated in the patterns during the search. This problem
could potentially be overcome by agreeing on how to specify acceptable
approximations when searching for minisatellites.
Some of these packages are implemented as Academic/Research Software
(ARS). Noting that ARS has a reputation of being difficult to use, this study
also investigated the usability of these ARS implementations. It relied on
literature that offers usability evaluation methods. Potential problems that
are likely to affect the general usability of the systems were identified. These
problems relate inter alia, to visibility, consistency and efficiency of use.
Furthermore, usability guidelines in the literature were followed to modify
the user interface of one of the implementations. A sample of users evaluated the before- and after versions of this user interface. Their feedback suggests
that the usability guidelines were indeed effective in enhancing the user
interface.
