PartiGene—constructing partial genomes (original) (raw)
Journal Article
School of Biological Sciences, Ashworth Laboratories, King's Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
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School of Biological Sciences, Ashworth Laboratories, King's Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
Search for other works by this author on:
School of Biological Sciences, Ashworth Laboratories, King's Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
Search for other works by this author on:
School of Biological Sciences, Ashworth Laboratories, King's Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
Search for other works by this author on:
School of Biological Sciences, Ashworth Laboratories, King's Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
Search for other works by this author on:
School of Biological Sciences, Ashworth Laboratories, King's Buildings, West Mains Rd, University of Edinburgh, Edinburgh EH9 3JT, UK
Search for other works by this author on:
Revision received:
09 December 2003
Accepted:
11 December 2003
Published:
26 February 2004
PDF Cite
John Parkinson, Alasdair Anthony, James Wasmuth, Ralf Schmid, Ann Hedley, Mark Blaxter, PartiGene—constructing partial genomes, Bioinformatics, Volume 20, Issue 9, June 2004, Pages 1398–1404, https://doi.org/10.1093/bioinformatics/bth101
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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 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).
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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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Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.