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Since the beginning of the genome project, the necessary involvement of scientists of widely divergent backgrounds has been evident. The proper handling, analysis, dissemination of information, and the control and data gathering of automated process are areas where computers are directly involved. Thus computers are intimately tied into the production and analysis of biological data. However, many challenges lie ahead.This volume is a collection of selected oral and poster presentations given at The Second International Conference on Bioinformatics, Supercomputing and Complex Genome Analysis, organized to address some of these challenges. The topics include the current status and future prospects of genome map, mapping and sequencing, complex genome analysis,linguistic and neural network approaches, database issues, and computer tools in the genome project. The volume will be ideal for students, newcomers, young researchers and experts alike, who are computationally or experimentally oriented.Keynote Speakers: C L Smith, D Grothues, T Ito, T Sano, D Wang, Y-W Zhu, C R Canton & R J Rohins.