MAGIC-SPP: A database-driven DNA sequence processing package with associated management tools
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Authors
Chun Liang
Feng Sun
Haiming Wang
Junfeng Qu
Robert M Freeman
Issue Date
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Journal Article, Academic Journal
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Keywords
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Abstract
Background: 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.
Results: 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 sufficiently long to justify doing so.
Conclusion: MAGIC-SPP has been designed to minimize human error, while simultaneously being
robust, versatile, flexible and automated. It offers a unique combination of features that permit
administration by a biologist with little or no informatics background. It is well suited to both
individual research programs and core facilities.