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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.

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introduction to bioinformatics ii

Introduction to Bioinformatics II

Lecture 12

Expressed Sequence Tags

By Ms. ShumailaAzam

expressed sequence tags ests
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 (“poor-man’s genome”)
  • EST annotations have very little biological information
slide3
EST…
  • An expressed sequence tag or EST is a short sub-sequence of a cDNAsequence.
  • 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
slide4

the ESTs represent portions of expressed genes.

  • cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand.
slide6

EST data repositories

dbESTrelease 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

Daniorerio (zebrafish) 1,350,105

Bostaurus (cattle) 1,318,208

Arabidopsis thaliana (thale cress) 1,276,692

Xenopus tropicalis 1,271,375

Oryzasativa (rice) 1,211,418

Zeamays (maize) 1,161,241

Triticumaestivum (wheat) 1,050,267

slide7

EST Applications

  • 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