Paper Info
Title
PartiGene---constructing partial genomes
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).
Year
DOI
Venue
2004
10.1093/bioinformatics/bth101
Bioinformatics
Keywords
Field
DocType
public domain,nucleic acid,sequence analysis,dna,expressed sequence tag,databases,expressed sequence tags,chromatography,sequence alignment
Sequence alignment,Genome,Data mining,Annotation,Expressed sequence tag,Suite,Computer science,Workstation,Software,Bioinformatics,Sequence analysis
Journal
Volume
Issue
ISSN
20
9
1367-4803
Citations 
PageRank 
References 
21
1.07
6
Authors
6
Name
Order
Citations
PageRank
John Parkinson1323.49
Alasdair Anthony2431.45
James Wasmuth3643.65
Ralf Schmid4802.82
Ann Hedley5361.42
Mark Blaxter618912.91