Software
MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools
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* Corresponding author: Lee H Pratt lpratt@plantbio.uga.edu
1 Laboratory for Genomics and Bioinformatics, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
2 Department of Computer Science, University of Georgia, Athens, GA 30602, USA
3 Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
4 Department of Botany, Miami University, Oxford, OH 45056, USA
5 Nanosphere, Inc., 4088 Commercial Avenue, Northbrook, IL 60062, USA
6 Department of Genetics, University of Georgia, Athens, GA 30602, USA
BMC Bioinformatics 2006, 7:115 doi:10.1186/1471-2105-7-115
Published: 7 March 2006Abstract
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.