Computational comparative analysis framework at the Centre for Bioinformatics and Biological Computing.

M Bellgard1, A Hunter2, D Schibeci, CBBC, Murdoch University;, CBBC, Murdoch University

The Centre for Bioinformatics and Biological Computing (CBBC) at Murdoch University conducts research in computational biology ranging from comparative genomic sequence analysis (eg. Kulski et. al., 2003, Bellgard, et. al., 2001), novel bioinformatics algorithms and software (eg. Bellgard, et. al, 2003a, Carter, 2001, Carter and Bellgard, 2003, Bellgard et. al., 2003b), and microarray and proteomic data analysis (eg. Bellgard et. al., 2003b, Schibeci, et. al., 2001).

In this context, the CBBC is striving to develop a computational comparative analysis framework that streamlines typical bioinformatics analysis, is flexible to incorporate data emanating from different biotechnologies, conducts audit trails on bioinformatics analysis, as well as facilitating distributed resource management.

We have developed a system referred to as YABI that facilitates hypothesis-driven comparative analysis, analysis audit trailing and allows for the creation bioinformatics pipelines. Where appropriate we link in open source tools and concepts. For example, we have incorporated a version of the DAS server and viewer (Stein et. al., 2002). We have also developed the GRENDEL system for distributed resource management based on the Sun Grid Engine that provides a single entry point for computational tasks while keeping the actual resources transparent to the user. In this way, we are able to obtain statistics on the amount and types of bioinformatics analysis and profile the computational implications and future requirements. We present an overview of this framework.

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References: M Bellgard , D Schibeci, E Trifonov and T Gojobori. Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. Journal of Molecular Evolution , Oct-Nov;53(4-5):465-8, (2001)

M Bellgard, T Gamble, M Reynolds, A Hunter, E Trifonov and R Taplin, Gap Mapping: A paradigm for sequence alignment, Applied Bioinformatics, to appear. (2003a).

M Bellgard , A Hunter, B Kenworthy, Microarray Analysis Using Bioinformatics Analysis Audit Trails (BAATs), Special Issue: From Functional Genomics to Systems Biology, Proceedings of the French Academy of Sciences, to appear, (2003b).

K Carter, A Oka, T Gen and M Bellgard. Bioinformatics issues for automating the annotation of genomic sequences. Genome Informatics Workshop, Tokyo, Japan, Dec. 19-21, 12:204-11, (2001).

K Carter and M Bellgard, MASV Multiple (BLAST) Annotation System Viewer, Bioinformatics, to appear, (2003).

Y Kulski, E Lim, D Dunn and M Bellgard, Genomic and phylogenetic analysis of the S100-A7 (psoriasin) gene duplications within the region of the S100 gene cluster on human chromosome 1q21. Journal of Molecular Evolution, Apr;56(4):397-406, (2003).

D Schibeci, R Potter, K Wathen-Dunn, M Jones and M Bellgard. Applying Artificial Neural Networks to the Classification of Wheat Varieties Processed Via MALDI-TOF Mass Spectrometry. Proceedings of the Neural Networks Applications ( NNA'01 ), Tenerife, Canary Islands, (2001).

LD Stein, S Eddy, and R Dowell, Distributed Sequence Annotation System (DAS) [online]