Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 60

comprehensive and rapid accumulation of cDNA clones, together with mass data
sets of their sequence tags have become important resources for functional genom-
ics (Boguski et al. 1993 ). ESTs derived from tissues in a range of developmental
stages or under various kinds of stress could significantly facilitate discovery of
new genes and their function. For example, large-scale expression analysis, genome
comparative DNA sequences and the design of expressed gene-specific molecular
markers and probes for microarrays have only been possible with extensive EST
data (Zhang et al. 2004 ; Kawaura et al. 2006 ; Mochida et al. 2006 ). Listed below
are a number of important web-based sites for RNA analysis and ESTs; and for ease
their purpose and URL are detailed in Table 2.3 .
TriMEDB
The Triticeae Mapped EST database (TriMEDB) provides information regarding
mapped cDNA motifs, which are related to barley and wheat sequences (Mochida
et al. 2008 ); a similar database, TriFLDB has much the same information (Mochida
et al. 2009b ).
NCBI—dbEST (Expressed Sequence Tag)
There are over 63 million ESTs in the NCBI dbEST databank, a most important
public domain EST database that includes a number of crop plant species (Boguski
et al. 1993 ). The data sets obtained from representative transcripts can be used as
unified transcript and sequence data, in line with other web sites below (Lee et al.
2005 ; Close et al. 2007 ; Duvick et al. 2008 ).
NCBI—UniGene
Identifies transcripts from the same locus as expressed in different types of tissue,
age or health status. Most importantly it reports not only on ESTs, but also on re-
lated proteins and clone resources.
TIGR
Plant transcript assemblies and gene indices web site. The databank relies on EST/
cDNA sequences linked to GenBank from NCBI. New releases and new plant data-
bases are documented regularly.