ScienceAsia 25 (1999) : 023-029 |doi: 10.2306/scienceasia1513-1874.1999.25.023

An Example in Kleisli:
Codon Usage Extraction Made Easy

Jiren Wang and Limsoon Wong

ABSTRACT: Codon usage information was useful to many molecular biologists in designing appropriate degenerate oligonucleotides and in optimizing expression of genes. It could also be used in improving the sensitivity of alignment tools in detection of short coding regions. We had two objectives in this paper. First, we wanted to build a system that could extract coding sequences of a specified organism from public DNA sequence databases and could compute their codon usage. Second, we wanted to demonstrate how the general database integration system called Kleisli could help build such a system and other sophisticated bioinformatics applications easily. We achieved these two objectives by showing that short and clear programs could be written in Kleisli, using its high-level query language CPL, to build such a system. The codon usage information of rice was produced as an example.

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BioInformatics Centre & Kent Ridge Digital Labs, 21 Heng Mui Keng Terrace, Singapore 119613 Email: jrwang@krdl.org.sg, limsoon@krdl.org.sg

Received 1 Feb 1999