Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 61

Table 2.3 Integrative databases for RNA and Expressed Sequence Tag (EST) analysis in plants
Database Name Plant Species/Purpose Uniform Resource Locator

(URL)

TriMEDB:Triticeae
Mapped EST DataBase
ver.2.0

Triticeae EST database; over
6000 sequences

http://trimedb.psc.riken.jp/
index.pl

NCBI dbEST EST of the extensive databank

from NCBI; multi species

http://www.ncbi.nlm.nih.gov/
dbEST/

Home—UniGene—NCBI Unigene (EST) comparison site

from NCBI; multi species

http://www.ncbi.nlm.nih.gov/
unigene

TIGR Plant Transcript
Assemblies

TA and EST of many plants,
including conifers, algae,
monocots and dicots

http://plantta.jcvi.org/

DFCI—Plant Gene Indices Plant gene indices (similar to
TA) of 60 important agricul-
tural plants

http://compbio.dfci.harvard.
edu/tgi/plant.html

HarvEST Home Page EST database of 10 of the most

important agricultural/horti-
cultural plants

http://harvest.ucr.edu/

HARVEST-BLAST.ORG HarvEST Blast search software

from NCBI

http://www.harvest-blast.org/

Plant MicroRNA Database Plant micro RNA website and
database of some commer-
cial plants

http://bioinformatics.cau.edu.
cn/PMRD/

Diversity Arrays Technol-
ogy Pty Ltd (DArT
P/L) | Diversity Arrays
Technology

Analysis of molecular diversity;
SNP, SSR, AFLP, RFLP,
methylation

http://www.diversityarrays.com/
index.html

Home | Affymetrix GeneChip mi RNA arrays

information—Affymetrix

http://www.affymetrix.com/
estore/

miRNA Array | Noncoding
RNA | Affymetrix

GeneChip mi RNA information
and species

http://www.affymetrix.com/
estore/browse/products.
jsp?productId=131473#1_1

GeneChip Medicago
Genome Array |
Affymetrix

Medicago GeneChip array and
its symbiont

http://www.affymetrix.
com/browse/products.
jsp?productId=131472#1_1

GoldenGate Genotyping
Assay—A flexible, pre-
optimized assay

Site for Golden Gate genotype
assay

http://www.illumina.com/tech-
nology/goldengate_genotyp-
ing_assay.ilmn

Illumina—Assay
Technology

Golden Gate genotype technol-
ogy information

http://www.illumina.com/com-
pany/assay_technology.ilmn

Illumina Genotyping High-throughput SNP

genotyping—Illumina

http://dnatech.genomecenter.
ucdavis.edu/illumina.html

CLC Biology Multi-purpose gene work

bench; with downloads

http://www.clcbio.com/index.
php?id=354