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 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

Photomorphogenic mutants of tomato

Photomorphogenesis of tomato is being studied with the aid of mutants which are either modified in their photore- ceptor composition or in their signal transduction chain(s) . Several mutants affecting the phytochrome family of photoreceptors, some of which appear deficient for specific genes encoding phytochrome apoproteins have been isolated . In addition, other mutants, including transgenic lines overexpressing phytochrome A, exhibit exaggerated photomorphogenesis during de-etiolation . Anthocyanin biosynthesis and plastid development are being used as model systems for the dissection of the complex interactions among photomorphogenic photoreceptors and to elucidate the nature of their transduction chains

Identification of two loci involved in phytochrome expression in Nicotiana plumbaginifolia and lethality of the corresponding double mutant

International audienc