Skip to main content
SpringerLink
Log in

Expressed Sequence Tags: An Overview

  • Protocol
  • First Online:
Expressed Sequence Tags (ESTs)

Part of the book series: Methods in Molecular Biology ((MIMB,volume 533))

Abstract

Expressed sequence tags (ESTs) are fragments of mRNA sequences derived through single sequencing reactions performed on randomly selected clones from cDNA libraries. To date, over 45 million ESTs have been generated from over 1400 different species of eukaryotes. For the most part, EST projects are used to either complement existing genome projects or serve as low-cost alternatives for purposes of gene discovery. However, with improvements in accuracy and coverage, they are beginning to find application in fields such as phylogenetics, transcript profiling and proteomics. This volume provides practical details on the generation and analysis of ESTs. Chapters are presented which cover creation of cDNA libraries; generation and processing of sequence data; bioinformatics analysis of ESTs; and their application to phylogenetics and transcript profiling.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Putney, S. D., Herlihy, W. C., and Schimmel, P. (1983) A new troponin T and cDNA clones for 13 different muscle proteins, found by shotgun sequencing. Nature 302, 718–21.

    Article  PubMed  CAS  Google Scholar 

  2. Adams, M. D., Kelley, J. M., Gocayne, J. D., Dubnick, M., Polymeropoulos, M. H., Xiao, H., Merril, C. R., Wu, A., Olde, B., Moreno, R. F., et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651–6.

    Article  PubMed  CAS  Google Scholar 

  3. Boguski, M. S., Lowe, T. M., and Tolstoshev, C. M. (1993) dbEST-database for “expressed sequence tags”. Nat Genet 4, 332–3.

    Article  PubMed  CAS  Google Scholar 

  4. Bernal, A., Ear, U., and Kyrpides, N. (2001) Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res 29, 126–7.

    Article  PubMed  CAS  Google Scholar 

  5. Ranjit, N., Jones, M. K., Stenzel, D. J., Gasser, R. B., and Loukas, A. (2006) A survey of the intestinal transcriptomes of the hookworms, Necator americanus and Ancylostoma caninum, using tissues isolated by laser microdissection microscopy. Int J Parasitol 36, 701–10.

    Article  PubMed  CAS  Google Scholar 

  6. Parkinson, J., Anthony, A., Wasmuth, J., Schmid, R., Hedley, A., and Blaxter, M. (2004) PartiGene – constructing partial genomes. Bioinformatics 20, 1398–404.

    Article  PubMed  CAS  Google Scholar 

  7. Wasmuth, J. D., and Blaxter, M. L. (2004) prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 5, 187.

    Article  PubMed  Google Scholar 

  8. Koski, L. B., Gray, M. W., Lang, B. F., and Burger, G. (2005) AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics 6, 151.

    Article  PubMed  Google Scholar 

  9. Eddy, S. R. (1998) Profile hidden Markov models. Bioinformatics 14, 755–63.

    Article  PubMed  CAS  Google Scholar 

  10. Parkinson, J., Whitton, C., Schmid, R., Thomson, M., and Blaxter, M. (2004) NEMBASE: a resource for parasitic nematode ESTs. Nucleic Acids Res 32, D427–30.

    Article  PubMed  CAS  Google Scholar 

  11. Wylie, T., Martin, J. C., Dante, M., Mitreva, M. D., Clifton, S. W., Chinwalla, A., Waterston, R. H., Wilson, R. K., and McCarter, J. P. (2004) Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res 32, D423–6.

    Article  PubMed  CAS  Google Scholar 

  12. Wheeler, D. L., Church, D. M., Federhen, S., Lash, A. E., Madden, T. L., Pontius, J. U., Schuler, G. D., Schriml, L. M., Sequeira, E., Tatusova, T. A., and Wagner, L. (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res 31, 28–33.

    Article  PubMed  CAS  Google Scholar 

  13. Lee, Y., Tsai, J., Sunkara, S., Karamycheva, S., Pertea, G., Sultana, R., Antonescu, V., Chan, A., Cheung, F., and Quackenbush, J. (2005) The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res 33, D71–4.

    Article  PubMed  CAS  Google Scholar 

  14. Peregrin-Alvarez, J. M., Yam, A., Sivakumar, G., and Parkinson, J. (2005) PartiGeneDB – collating partial genomes. Nucleic Acids Res 33, D303–7.

    Article  PubMed  CAS  Google Scholar 

  15. Parkinson, J., and Blaxter, M. (2003) SimiTri – visualizing similarity relationships for groups of sequences. Bioinformatics 19, 390–5.

    Article  PubMed  CAS  Google Scholar 

  16. Kenyon, F., Welsh, M., Parkinson, J., Whitton, C., Blaxter, M. L., and Knox, D. P. (2003) Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis – allergens, proteases and free-radical scavengers. Parasitology 126, 451–60.

    Article  PubMed  CAS  Google Scholar 

  17. Fernandez, C., Gregory, W. F., Loke, P., and Maizels, R. M. (2002) Full-length-enriched cDNA libraries from Echinococcus granulosus contain separate populations of oligo-capped and trans-spliced transcripts and a high level of predicted signal peptide sequences. Mol Biochem Parasitol 122, 171–80.

    Article  PubMed  CAS  Google Scholar 

  18. Luo, M., Dang, P., Guo, B. Z., He, G., Holbrook, C. C., Bausher, M. G., and Lee, R. D. (2005) Generation of Expressed Sequence Tags (ESTs) for gene discovery and marker development in cultivated peanut. Crop Sci 45, 346–53.

    Article  CAS  Google Scholar 

  19. Wong, C. E., Li, Y., Whitty, B. R., Diaz-Camino, C., Akhter, S. R., Brandle, J. E., Golding, G. B., Weretilnyk, E. A., Moffatt, B. A., and Griffith, M. (2005) Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap. Plant Mol Biol 58, 561–74.

    Article  PubMed  CAS  Google Scholar 

  20. Jenny, M. J., Ringwood, A. H., Lacy, E. R., Lewitus, A. J., Kempton, J. W., Gross, P. S., Warr, G. W., and Chapman, R. W. (2002) Potential indicators of stress response identified by expressed sequence tag analysis of hemocytes and embryos from the American oyster, Crassostrea virginica. Mar Biotechnol (NY) 4, 81–93.

    Article  CAS  Google Scholar 

  21. Sturzenbaum, S., Parkinson, J., Blaxter, M., Morgan, A., Kille, P., and Georgiev, O. (2003) The earthworm EST sequencing project. Pedobiologia 47, 447–51.

    Google Scholar 

  22. Li, L., Brunk, B. P., Kissinger, J. C., Pape, D., Tang, K., Cole, R. H., Martin, J., Wylie, T., Dante, M., Fogarty, S. J., Howe, D. K., Liberator, P., Diaz, C., and erson, J., White, M., Jerome, M. E., Johnson, E. A., Radke, J. A., Stoeckert, C. J., Jr., Waterston, R. H., Clifton, S. W., Roos, D. S., and Sibley, L. D. (2003) Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database. Genome Res 13, 443–54.

    Article  PubMed  Google Scholar 

  23. Hughes, J., Longhorn, S. J., Papadopoulou, A., Theodorides, K., de Riva, A., Mejia-Chang, M., Foster, P. G., and Vogler, A. P. (2006) Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Mol Biol Evol 23, 268–78.

    Article  PubMed  Google Scholar 

  24. Parkinson, J., Mitreva, M., Whitton, C., Thomson, M., Daub, J., Martin, J., Schmid, R., Hall, N., Barrell, B., Waterston, R. H., McCarter, J. P., and Blaxter, M. L. (2004) A transcriptomic analysis of the phylum Nematoda. Nat Genet 36, 1259–67.

    Article  PubMed  Google Scholar 

  25. Ghedin, E., Wang, S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J. E., Delcher, A. L., Guiliano, D. B., Miranda-Saavedra, D., Angiuoli, S. V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N. M., Wortman, J. R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S. L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G. J., Carlow, C. K., Crawford, M. J., Daub, J., Dimmic, M. W., Estes, C. F., Foster, J. M., Ganatra, M., Gregory, W. F., Johnson, N. M., Jin, J., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B. W., Li, W., Lindblom, T. H., Lustigman, S., Ma, D., Maina, C. V., Martin, D. M., McCarter, J. P., McReynolds, L., Mitreva, M., Nutman, T. B., Parkinson, J., Peregrin-Alvarez, J. M., Poole, C., Ren, Q., Saunders, L., Sluder, A. E., Smith, K., Stanke, M., Unnasch, T. R., Ware, J., Wei, A. D., Weil, G., Williams, D. J., Zhang, Y., Williams, S. A., Fraser-Liggett, C., Slatko, B., Blaxter, M. L., and Scott, A. L. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science 317, 1756–60.

    Article  PubMed  CAS  Google Scholar 

  26. LoVerde, P. T., Hirai, H., Merrick, J. M., Lee, N. H., and El-Sayed, N. (2004) Schistosoma mansoni genome project: an update. Parasitol Int 53, 183–92.

    Article  PubMed  CAS  Google Scholar 

  27. Philippe, H., Lartillot, N., and Brinkmann, H. (2005) Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol 22, 1246–53.

    Article  PubMed  CAS  Google Scholar 

  28. Peregrin-Alvarez, J. M., and Parkinson, J. (2007) The global landscape of sequence diversity. Genome Biol 8, R238.

    Article  PubMed  Google Scholar 

  29. Zhang, Y., Eberhard, D. A., Frantz, G. D., Dowd, P., Wu, T. D., Zhou, Y., Watanabe, C., Luoh, S. M., Polakis, P., Hillan, K. J., Wood, W. I., and Zhang, Z. (2004) GEPIS – quantitative gene expression profiling in normal and cancer tissues Bioinformatics 20, 2390–8.

    Article  PubMed  CAS  Google Scholar 

  30. Ferguson, D. A., Chiang, J. T., Richardson, J. A., and Graff, J. (2005) eXPRESSION: an in silico tool to predict patterns of gene expression. Gene Expr Patterns 5, 619–28.

    Article  PubMed  CAS  Google Scholar 

  31. Stanton, J. A., Macgregor, A. B., and Green, D. P. (2003) Identifying tissue-enriched gene expression in mouse tissues using the NIH UniGene database. Appl Bioinformatics 2, S65–73.

    PubMed  CAS  Google Scholar 

  32. Ramsey, J. S., Wilson, A. C., de Vos, M., Sun, Q., Tamborindeguy, C., Winfield, A., Malloch, G., Smith, D. M., Fenton, B., Gray, S. M., and Jander, G. (2007) Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design. BMC Genomics 8, 423.

    Article  PubMed  Google Scholar 

  33. Gracey, A. Y., Fraser, E. J., Li, W., Fang, Y., Taylor, R. R., Rogers, J., Brass, A., and Cossins, A. R. (2004) Coping with cold: an integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci USA 101, 16970–5.

    Article  PubMed  CAS  Google Scholar 

  34. Owen, J., Hedley, B., Svendsen, C., Wren, J., Jonker, M. J., Hankard, P. K., Lister, L. J., Stu¨rzenbaum, S. R., Morgan, A. J., Spurgeon, D. J., Blaxter, M. L., and Kille, P. (2008) Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus. BMC Genomics. 9, 266.

    Google Scholar 

  35. Edwards, N. J. (2007) Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol Syst Biol 3, 102.

    PubMed  Google Scholar 

  36. Gupta, S., Zink, D., Korn, B., Vingron, M., and Haas, S. A. (2004) Genome wide identification and classification of alternative splicing based on EST data. Bioinformatics 20, 2579–85.

    Article  PubMed  CAS  Google Scholar 

  37. Ner-Gaon, H., Leviatan, N., Rubin, E., and Fluhr, R. (2007) Comparative cross-species alternative splicing in plants. Plant Physiol 144, 1632–41.

    Article  PubMed  CAS  Google Scholar 

  38. Panitz, F., Stengaard, H., Hornshoj, H., Gorodkin, J., Hedegaard, J., Cirera, S., Thomsen, B., Madsen, L. B., Hoj, A., Vingborg, R. K., Zahn, B., Wang, X., Wang, X., Wernersson, R., Jorgensen, C. B., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., Green, T., Nielsen, B. J., Havgaard, J. H., Brunak, S., Fredholm, M., and Bendixen, C. (2007) SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinformatics 23, i387–91.

    Article  PubMed  CAS  Google Scholar 

  39. Tang, J., Vosman, B., Voorrips, R. E., van der Linden, C. G., and Leunissen, J. A. (2006) QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 7, 438.

    Article  PubMed  Google Scholar 

  40. Huntley, D., Baldo, A., Johri, S., and Sergot, M. (2006) SEAN: SNP prediction and display program utilizing EST sequence clusters. Bioinformatics 22, 495–6.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada

    John Parkinson

  2. Departments of Biochemistry & Molecular Genetics, University of Toronto, Toronto, ON, Canada

    John Parkinson

  3. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK

    Mark Blaxter

Authors
  1. John Parkinson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mark Blaxter
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Molecular Structure and Function Hospital for Sick Children, Departments of Biochemistry & Molecular Genetics, University of Toronto, Toronto, ON, Canada

    John Parkinson

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Parkinson, J., Blaxter, M. (2009). Expressed Sequence Tags: An Overview. In: Parkinson, J. (eds) Expressed Sequence Tags (ESTs). Methods in Molecular Biology, vol 533. Humana Press. https://doi.org/10.1007/978-1-60327-136-3_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-136-3_1

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-759-4

  • Online ISBN: 978-1-60327-136-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation