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Bioinformatics Advance Access published online on February 26, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth101
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 31, 2003
Revised December 9, 2003
Accepted December 11, 2003

Article

PartiGene--constructing partial genomes

John Parkinson 1*, Alasdair Anthony 1, James Wasmuth 1, Ralf Schmid 1, Ann Hedley 1, Mark Blaxter 1

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

* To whom correspondence should be addressed. E-mail: jparkin{at}sickkids.ca.


  Abstract

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 organising this data within a genomic context to facilitate large scale analyses. Here we present PartiGene, an integrated sequence analysis suite which 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 customisable 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).


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