Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 87

GTOP
Databases housing previously predicted structures from amino acid sequences by
template-based modelling for a wide range of species exist on this site; the Genome
TO Protein structure and function (GTOP) database. Data in this site is obtained
by the application of various computational tools for structural prediction from se-
quences of amino acids and genomes (Fukuchi et al. 2009 ).
CATH/SCOP
The databases for structure-related protein classification, as typified by CATH and
the Structural Classification of Proteins (SCOP) data sites, have provided important
clues to the relationship between proteins, protein function and protein evolution
(Greene et al. 2007 ; Andreeva et al. 2008 ).
PANTHER
A database for protein families based on conserved protein domains, the Protein
Analysis Through Evolutionary Relationships (PANTHER) is an important site for
classifying proteins into families. The database contains the evolution and function
of proteins, and the resources are used in genome-wide identification of genes (Mi
et al. 2005 ; Wilson et al. 2007 ; Finn et al. 2008 ; Wilson et al. 2008 ).
Plant-Metabolism (Metabolomics)
Metabolomics is referred to as an understanding of metabolism primarily based on
comprehensive and multidimensional approaches, by taking advantage of various
analytical instruments and bioinformation available to identify metabolites. Metab-
olomic data can include individual and multiple assessments of metabolites, and to
quantify particular metabolites in order to provide advantages over chemical pheno-
type analysis. The plant metabolome is complex enough for an individual plant, but
it is even more challenging for comparison between plants (Bino et al. 2004 ; von
Roepenack-Lahaye et al. 2004). Therefore, plant metabolomics is a great analyti-
cal challenge, but nevertheless it is important to an understanding of plant growth
and development. Metabolomics has the ability to improve knowledge of plant cell
systems, to engineer molecular breeding and to improve the productivity and func-
tion of plants in areas like stress tolerance, pharmaceutical production, food quality,
biomaterials and energy (Trethewey 2004 ; Oksman-Caldentey and Saito 2005 ; Fer-
nie and Schauer 2009 ). In this section, we include metabolomic analytical sites for
plants, metabolic profiling, instrumentation and their applications with respect to
other 'omics' research. We also describe plant metabolomics related computational
tools and databases commonly in use.