As the number of available genome sequences increases, comparative bioinformatics analysis becomes more and more instructive. However, such an analysis is difficult to carry out without a suitable platform gathering not only curated annotation results using standardized computational methods but also key relevant information obtained by applying carefully designed bioinformatics methods. With the aim of solving these difficulties, our group is developing a web-based computational system named iCAT (integrated Comparative Analysis Tool) to collect, analyse, centralize and integrate genomic and related data and bibliographic information. After selecting a set of genomes, the user can launch various types of search based on annotation, position on the chromosomes or sequence similarity. In addition, relationships of putative orthology will be precomputed to allow differential genome queries. Specific tools are available and will also be continuously developed for the graphical visualization of the results, including a multi-genome browser for displaying dynamic pictures with clickable objects and for viewing relationships of precomputed similarity. The bioinformatics resources and strategies for analysing the annotation and re-annotation of genome sequences and defining comparative relationships often require novel bioinformatics analysis, integration and interoperability of local/third party data and information resources as well as analysis and visualization tools. Interoperability is a key issue for information to be available at the right time. Our iCAT system for genomic data is created exactly to fulfill this purpose and is designed to integrate all the complete genomes as they become available.
Assistant Professor and Director of Bioinformatics Program, Institute of Bioinformatics, National Yang-Ming University,Taipei, Taiwan 11221, R.O.C.
I received my PhD in Molecular Biology from University of Southern California, followed by a post-doctoral research in breast cancer-related oncogenes at the Cancer Research Center, University of California, San Francisco. I then worked for the Industrial Technology Research Institute (ITRI) for three years. At ITRI, I had led the Genomics Department to develop a bioinformatics pipeline for microbial genome annotation and a fever-chip using microarray technology for identifying infectious pathogens. In 2002, I became an assistant professor at the Institute of Genetics, National Yang-Ming University. Since 2003 I have been an assistant professor at the Institute of Bioinformatics. In the past few years, our Comparative Bioinformatics team has established an integrated comparative bioinformatics infrastructure for genome annotation/re-annotation and comparative analysis.