MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools

BMC Bioinformatics
Chun LiangMarie-Michèle Cordonnier-Pratt

Abstract

Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the flexible, scalable, and automated sequence processing package described here. MAGIC-SPP is a DNA sequence processing package consisting of an Oracle 9i relational database, a Perl pipeline, and user interfaces implemented either as JavaServer Pages (JSP) or as a Java graphical user interface (GUI). The database not only serves as a data repository, but also controls processing of trace files. MAGIC-SPP includes an administrative interface, a laboratory information management system, and interfaces for exploring sequences, monitoring quality control, and troubleshooting problems related to sequencing activities. In the sequence trimming algorithm it employs new features designed to improve performance with respect to concerns such as concatenated linkers, identification of the expected start position of a vector insert, and extending the useful length of trimmed sequences by bridging short regions of low quality when the following high quality segment is ...Continue Reading

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Citations

May 10, 2007·Nucleic Acids Research·Chun LiangJeffrey F D Dean
Sep 28, 2007·BMC Bioinformatics·Michael C WendlRichard K Wilson
Mar 10, 2011·BMC Research Notes·Peter V TroshinGeoffrey J Barton
Jun 15, 2007·Systematic Biology·Frank KauffFrançois Lutzoni
Nov 14, 2007·The Journal of Biological Chemistry·Scott R BaersonStephen O Duke

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Methods Mentioned

BETA
384-well sequencing

Software Mentioned

Lucy
QualityAnalysisContro l
MAGIC SEQ - LIMS
SequenceRead
PolyT
Plate Viewer
Tomcat
Status Report
J2SE
ESTprep

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