Principles of Plant Genetics and Breeding

sequence analysis. It is an application of information
science to biology. It uses supercomputers and sophisticated
software to search and analyze databases accumulated
from genome sequencing projects and other similar
efforts. Bioinformatics allows scientists to make predictions
based on previous experiences with biological
reality. In one application, the biological information
bank is searched to find sequences with known function
that resemble the unknown sequence and thereby predict
the function of the unknown sequence. Databases
are critical to bioinformatics and hence repositories exist
in various parts of the world for genetic sequence data.
Types of bioinformatics databases
Information used in bioinformatics research may be
grouped into two categories:
1 Primary databases. These databases consist of original
biological data such as raw DNA sequences and
protein structure information from crystallography.
2 Secondary databases. These databases contain original
data that have been processed to suit certain
specific applications.
To be useful, a good database should have two critical
parts: (i) the original sequence; and (ii) and an annotation
description of the biological context of the data. It
is critical that each entry be accompanied by a detailed
and complete annotation, without which a bioinformatics
search becomes an exercise in futility since it would
be difficult to assign valid meaning to any relationships
discovered. Some databases include taxonomic information
such as the structural and biochemical characteristics
of organisms.
The bulk of data in repositories consist of primary
data. Three major entities are collaboratively responsible
for maintaining gene sequence databases. These entities
are the European Molecular Biology Lab (EMBL) of
Cambridge, UK, the GeneBank of the National Center
for Biotechnology Information (NCBI) that is affiliated
with the National Institutes of Health, USA, and the
DNA Databank of Japan.
Databases for both protein sequences and structure
are being maintained. The Department of Medical
Biochemistry (University of Geneva) and European
Bioinformatics Institute collaboratively maintain properly
annotated translations of sequences in the EMBL
databases. This is called the SWISSPROT. TREMBL is
another protein database consisting solely of proteincoding
regions of the EMBL database (called the translated
EMBL or TREMBL). The NCBI also maintains a
BIOTECHNOLOGY IN PLANT BREEDING 239
database of the translations of the GeneBank. Another
kind of protein database consisting of experimentally
derived 3D structures of proteins is kept at the protein
databank where these structures are determined by Xray
diffraction and nuclear magnetic resonance.
General steps in a bioinformatics project
One purpose of searching a bioinformatics database is to
determine if the researcher’s unknown sequence, DNA
or protein, matches any sequence in the database in
terms of structure or function. This requires the proper
choice and skillful use of software to align the unknown
sequence with the known. Gene-seeking software varies
in capability and ease of use. They have certain properties
in common: (i) algorithms for pattern recognition
use statistical probability analysis to determine the similarity
between two sequences; (ii) data tables contain
information on consensus sequences for various genetic
elements; (iii) taxonomic differences are included because
consensus sequences vary between different taxonomic
classes to facilitate analysis and minimize errors; and (iv)
specific instructions describe how the algorithms should
be applied in an analysis and how the results should be
interpreted.
A search involves two key activities:
1 Sequence alignment scoring matrices. The unknown
sequence is aligned with those in the bank. Scores
are assigned on the basis of the sequence homology
detected. It is most useful to align sequences such
that the largest scores are assigned to the most
biologically significant matches.
2 Comparing sequences against a database. One
of the most common searches of bioinformatics
databases is to compare an unknown sequence
against those in the database to discover similarities.
Typical homology search algorithms are used in this
activity. Some of the most widely used software for
this search is the Basic Local Alignment Search Tool
(BLAST) and FASTA. BLAST uses a strategy based
on short sequence fragments between the unknown
sequence and those in the database. It is designed
to match only continuous sequences (no gaps from
deletion or insertion mutations are taken into
account).
DNA microarrays in plant breeding
Genes are not only variably expressed, but the level of
expression varies during a physiological change, some