Hunting TPR Domains Using Kleisli

Kui Lin[1] (linkui@bic.nus.edu.sg)
Anthony E. Ting[2] (mcbaet@imcb.nus.edu.sg)
Jiren Wang[3] (jrwang@krdl.org.sg)

[1] NUS BioInformatics Center, National University of Singapore
Singapore 119260
[2] Institute of Molecular & Cell Biology, 30 Medical Drive
Singapore 117609
[3] Kent Ridge Digital Labs,21 Heng Mui Keng Terrace
Singapore 119613


Abstract

We have two objectives. First, we want to build a system for detecting tetratricopeptide repeats in protein sequences. Second, we want to demonstrate how the general bioinformatics database integration system called Kleisli can help build such a system easily. We achieve these two objectives by showing that short and clear programs can be written in Kleisli, using its high-level query language CPL, to build a TPR domain hunter by integrating WU-BLAST2.0, HMMER, Entrez, and PFAM.

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Japanese Society for Bioinformatics