Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 55

24 plants; including 12 wild and domesticated rice genomes. An organelle data bank
is also available from this site (Sect. 4.5).
NCBI—Entrez
Tracks over 800 whole genome projects from biological organisms, and the 115
species of Viridiplantae; including agronomically important crops for food and
fruit, medicine and a number of green algae. The Entrez database can be accessed
through the home page of NCBI.
NCBI—BLAST
One of the most important sites and tools available, in determining base similari-
ties between nucleotide sequences in databanks. It also contains protein searches
and queries. It includes searches for translated nucleotide sequences, conserved do-
mains, multiple alignment tools, evolutionary relationships, and can be applied to
all organisms, or limited to specific plants.
GrainGenes and PlantGDB
GrainGenes is a specific database for Triticeae and Avena genes, markers, maps
and germplasm. PlantGDB contains sequences and a search engine linked to NCIB
BLAST for 15 Dicotyledon, 7 Monocotyledon and 3 other plant species. It contains
more limited information than the NCBI site over most plants, but is especially use-
ful for agricultural grain species.
DNASequencingandUltraHigh-Throughput
Genome sequence information aids researchers in identify genes and gene families,
including the identification of coding or non-coding regions, regulatory genes, and
repetitive sequences within the genome (e.g. simple sequence repeats—SSRs); all
of these are important in molecular biology. This type of information has become
primary material for the design of genome advancements, such as microarrays, till-
ing arrays or molecular and chromosome markers, and these methods are important
in whole plant genomic sequencing (Sect. 2.3 below). Pyrosequencing, massive
parallel DNA sequencing and single molecule sequencing are adaptations of exist-
ing methods, which have become available in recent years (Margulies et al. 2005 ;
Ansorge 2009 ). These new technologies have provided researchers with new meth-
ods to addressed web information in an entirely different way, and ongoing innova-
tions in next-generation sequencing technology (Sect. 2.3), and the release of new