Processing Sequence Annotation Data Using the Lua Programming Language

Yutaka Ueno[1],[2] (uenoyt@ni.aist.go.jp)
Masanori Arita[1],[3] (arita@k.u-tokyo.ac.jp)
Toshitaka Kumagai[1] (kuma@cbrc.jp)
Kiyoshi Asai[1],[3] (asai@k.u-tokyo.ac.jp)

[1]Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-43-17 Aomi, Koto-ku, Tokyo 135-0064, Japan
[2]Neuroscience Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1 Umezono, AIST Central 2, Tsukuba, Ibaragi 305-8568, Japan
[3]Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan


Abstract

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/.

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Japanese Society for Bioinformatics