title: MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratory for Genomics and Bioinformatics, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA. liangc@muohio.edu
authors.forename: Chun
authors.initials: C
authors.lastname: Liang
authors.forename: Feng
authors.initials: F
authors.lastname: Sun
authors.forename: Haiming
authors.initials: H
authors.lastname: Wang
authors.forename: Junfeng
authors.initials: J
authors.lastname: Qu
authors.forename: Robert M
authors.initials: RM
authors.lastname: Freeman
authors.forename: Lee H
authors.initials: LH
authors.lastname: Pratt
authors.forename: Marie-Michèle
authors.initials: MM
authors.lastname: Cordonnier-Pratt
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D016247:Information Storage and Retrieval / Q000379:methods*; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software