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Bioinformatics Advance Access originally published online on February 26, 2004
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Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.

PartiGene—constructing partial genomes

John Parkinson *, Alasdair Anthony , James Wasmuth , Ralf Schmid , Ann Hedley and Mark Blaxter

School of Biological Sciences, Ashworth Laboratories, King's Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK

Received on July 31, 2003; revised on December 9, 2003; accepted on December 11, 2003
Advance Access Publication February 26, 2004

Expressed sequence tags (ESTs) offer a low-cost approach to gene discovery and are being used by an increasing number of laboratories to obtain sequence information for a wide variety of organisms. The challenge lies in processing and organizing this data within a genomic context to facilitate large scale analyses. Here we present PartiGene, an integrated sequence analysis suite that uses freely available public domain software to (1) process raw trace chromatograms into sequence objects suitable for submission to dbEST; (2) place these sequences within a genomic context; (3) perform customizable first-pass annotation of the data; and (4) present the data as HTML tables and an SQL database resource. PartiGene has been used to create a number of non-model organism database resources including NEMBASE (http://www.nematodes.org) and LumbriBase (http://www.earthworms.org/). The packages are readily portable, freely available and can be run on simple Linux-based workstations.

Availability: PartiGene is available from http://www.nematodes.org/PartiGene and also forms part of the EST analysis software, associated with the Natural Environmental Research Council (UK) Bio-Linux project (http://envgen.nox.ac.uk/biolinux.html).

Contact: jparkin{at}sickkids.ca

* To whom correspondence should be addressed at Programs in Genetics, Genomic Biology & Structural Biology, Biochemistry, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada.


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