PartiGene-constructing partial genomes

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

Research output: Contribution to journalArticlepeer-review

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).
Original languageEnglish
Pages (from-to)1398-404
Number of pages7
JournalBioinformatics
Volume20
Issue number9
DOIs
Publication statusPublished - 2004

Keywords

  • Chromatography
  • Chromosome Mapping
  • Databases, Nucleic Acid
  • Expressed Sequence Tags
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology
  • Software
  • User-Computer Interface

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