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EST Processing: From Trace to Sequence

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Expressed Sequence Tags (ESTs)

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

Abstract

A common task in EST projects is the conversion of sequence chromatograms originating from gel-based or capillary sequencers into annotated sequence objects. Here we describe the usage of a software pipeline (available from http://www.nematodes.org/bioinformatics/), which has been developed to make the most of EST datasets. This modular software solution is targeted toward small- to medium-sized EST projects and comprises a series of Perl scripts. The software design is based on our experience during EST projects for parasitic nematodes and other species. The trace2dbest module processes sequence trace files and prepares the text files necessary for the submission of the sequences to the public repository dbEST. PartiGene provides facilities for clustering and assembling the ESTs into putative gene objects or unigenes and organizes the data in a relational database. Additional tools are available for annotation and for making the data accessible via the World Wide Web.

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Acknowledgements

The authors would like to thank all contributors and users of trace2dbest, PartiGene, and other tools of the Edinburgh EST pipeline, in particular Alasdair Anthony, John Parkinson, James Wasmuth, and Ann Hedley. Funding was in part from the NERC Environmental Genomics Thematic Data Program.

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Authors and Affiliations

  1. Department of Biochemistry, University of Leicester, Leicester, UK

    Ralf Schmid

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

    Mark Blaxter

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  1. Ralf Schmid
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  2. Mark Blaxter
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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

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

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Schmid, R., Blaxter, M. (2009). EST Processing: From Trace to Sequence. 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_9

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  • DOI: https://doi.org/10.1007/978-1-60327-136-3_9

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-759-4

  • Online ISBN: 978-1-60327-136-3

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