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

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 p...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Chun Liang, Feng Sun, Haiming Wang, Junfeng Qu, Robert M. Freeman Jr, Lee H. Pratt, Marie-Michèle Cordonnier-Pratt
• Keywords: BMCBI 2006, Core Facilities, DNA Sequence, DNA Sequence Data