SpringerProtocols: Abstract: EST Processing: From Trace to Sequence

9. EST Processing: From Trace to Sequence

By: Ralf Schmid¹, Mark Blaxter²

Abstract

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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.

Affiliation(s): (1) Department of Biochemistry, University of Leicester, Leicester, UK
(2) Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK

Book Title: Expressed Sequence Tags (ESTs): Generation and Analysis

Series: Methods in Molecular Biology | Volume: 533 | Year: 2009 | Page Range: 1-32 | DOI: 10.1007/978-1-60327-136-3_9

Subject: Genetics/Genomics

Key Words: EST - expressed sequence tags - dbEST - Bioinformatics - PartiGene - trace2dbest

References

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