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Introduction to Bioinformatics II

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

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  1. Introduction to Bioinformatics II Lecture 12 Expressed Sequence Tags By Ms. ShumailaAzam

  2. 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

  3. 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

  4. the ESTs represent portions of expressed genes. • cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand.

  5. 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

  6. 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

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