Processing sequence annotation data using the Lua programming language.

The data processing language in a graphical software tool that manages sequence annotation data from genome databases should provide flexible functions for the tasks in molecular biology research. Among currently available languages we adopted the Lua programming language. It fulfills our requirements to perform computational tasks for sequence map layouts, i.e. the handling of data containers, symbolic reference to data, and a simple programming syntax. Upon importing a foreign file, the original data are first decomposed in the Lua language while maintaining the original data schema. The converted data are parsed by the Lua interpreter and the contents are stored in our data warehouse. Then, portions of annotations are selected and arranged into our catalog format to be depicted on the sequence map. Our sequence visualization program was successfully implemented, embedding the Lua language for processing of annotation data and layout script. The program is available at http://staff.aist.go.jp/yutaka.ueno/guppy/.

[1]  T Horiuchi,et al.  Functional genomics of Escherichia coli in Japan. , 2000, Research in microbiology.

[2]  Peter D. Karp,et al.  An Evaluation of Ontology Exchange Languages for Bioinformatics , 2000, ISMB.

[3]  Roderic Guigó,et al.  Gff2ps: Visualizing Genomic Annotations , 2000, Bioinform..

[4]  K Asai,et al.  Recognition of human genes by stochastic parsing. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[5]  W. H. Inmon,et al.  Building the data warehouse (2nd ed.) , 1996 .

[6]  Kim Rutherford,et al.  Artemis: sequence visualization and annotation , 2000, Bioinform..

[7]  Anthony Kosky,et al.  Seamless Integration of Biological Applications within a Database Framework , 1999, ISMB.

[8]  Stephen R. Gardner.  Building the data warehouse , 1998, CACM.

[9]  Jonathan Crabtree,et al.  bioWidgets: data interaction components for genomics , 1999, Bioinform..

[10]  Y Ueno,et al.  A high-throughput graphics library designed for a portable molecular structure viewer. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[11]  Emmanuel Barillot,et al.  XML, bioinformatics and data integration , 2001, Bioinform..

[12]  Bjarne Stroustrup,et al.  C++ Programming Language , 1986, IEEE Softw..

[13]  Roberto Ierusalimschy,et al.  Lua—An Extensible Extension Language , 1996, Softw. Pract. Exp..

[14]  Kiyoshi Asai,et al.  BESPA: Software Tools for Three-Dimensional Structure Reconstruction from Single Particle Images of Proteins , 1999 .

[15]  Peter D. Karp,et al.  A Strategy for Database Interoperation , 1995, J. Comput. Biol..

[16]  J M Ostell,et al.  The NCBI data model. , 2001, Methods of biochemical analysis.

[17]  D B Searls,et al.  bioTk:componentry for genome informatics graphical user interfaces. , 1995, Gene.