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Introduction to Bioinformatics II
Lecture 12
Expressed Sequence Tags
By Ms. Shumaila Azam
Expressed Sequence Tags (ESTs)
• Unedited, short, single pass sequences
generated from 5' or 3' end of randomly
selected cDNA libraries in desired
cells/tissues/organ.
• Length: 200-700 bp (average 360 bp)
• Can be quickly generated at low cost (“poorman’s genome”)
• EST annotations have very little biological
information
EST…
• An expressed sequence tag or EST is a short
sub-sequence of a cDNA sequence.
• They may be used
– to identify gene transcripts,
– and are instrumental in gene discovery
– and gene sequence determination.
• 74.2 million ESTs now available in public
databases
• the ESTs represent portions of expressed
genes.
• cDNA/mRNA sequence or as the reverse
complement of the mRNA, the template
strand.
EST data repositories
dbEST release 061507 (June, 2007) www.ncbi.nlm.nih.gov/dbEST/
43,396,096 ESTs from 659 different organisms
Homo sapiens (human) 8,119,106
Mus musculus (mouse) 4,850,243
Danio rerio (zebrafish) 1,350,105
Bos taurus (cattle) 1,318,208
Arabidopsis thaliana (thale cress) 1,276,692
Xenopus tropicalis 1,271,375
Oryza sativa (rice) 1,211,418
Zea mays (maize) 1,161,241
Triticum aestivum (wheat) 1,050,267
EST Applications
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Gene Discovery
Gene Structure Prediction
Expression Maps
Alternative Splicing
Identification and characterization of SNPs
Gene expression studies
tissue or disease specific
developmental stage
Proteomics (for example peptide mass fingerprinting)
Identification of drug and vaccine candidates