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Contact: Mohamad Musavi, Cristian Domnisoru, Habtom Ressom
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| The major goal in this project is to develop a new base calling technique to improve the efficiency of the DNA sequencing process. Improved efficiency will be achieved by increasing the average length of error-free sequences and enhancing the base identification process at the beginning and end of sequences. This will greatly increase sequencing throughput and reduce cost and error associated with the current DNA sequencing process. ABI machines that are currently the major source of reading DNA data are capable of producing sequences of 1000 bases in length. ABI associated software and Phred software that are used by the sequencing community are reliable and accurate. They can produce impressive results of 500~600 error-free sequences. The error-free sequences are normally located in the middle of the 1000 base length where the data is clear and bases are easily distinguishable. However, the bases at the beginning and end of a 1000 base sequence are obscure and difficult to identify. The base calling error in these regions is relatively high. Thus the average base calling error over a 1000 base sequence is between 3.5~6%. The foundation of our proposed research is based on new findings related to cross-talk filtering, mechanical shift phenomena, baseline adjustment, base-spacing prediction and the development of a neuro-fuzzy base-calling algorithm. The preliminary investigation of our proposed methodology on a limited test set has shown that the error-free length can be extended to 800 bases, a 30% improvement. In addition, it has been shown that the error rate in the hard-to-identify regions of sequences, the beginning and the end of sequences, can also be reduced. The overall effect of these two improvements has resulted in an error rate of less than 2% for our preliminary data. The error rate is expected to approach less than 1% by the implementation of adaptive capabilities to allow the operator to interactively correct the base calling errors so that the system doesn't make duplicate mistakes. Our plans are to fully develop and implement a new base-calling methodology. It will be tested and validated on a large number of DNA sequences. The methodology will be provided in base-calling software to be used by the DNA sequencing community as an alternative to ABI and Phred. The software will remove the dependency of current software on specific hardware or operating systems and be machine-independent for exploitation over the Web. This effort is a joint project between the University of Maine Intelligent System Laboratory (www.intsys.maine.edu) and the DNA Sequencing Facility (www.ume.maine.edu/dnaseq). Our joint work and expertise have given us a unique opportunity to effectively address an emergent need in the computational biology area. |
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Musavi, M.T., Domnisoru, C., Natarajan, P., Varghese, R., Toothaker, M., Dawood, J., Ressom, H., Van Beneden, R., Singer, P., "TraceTools: a new DNA basecaller," submitted
to Journal of Bioinformatics, Dec. 2003, a copy is available at www.intsys.maine.edu/AccurateDNA.htm.
Andrushkiv, R.I., H.R. Arabnia, J. Beatty, W.W. Bein, T. Cao-Huu, R.J. Dalpatadu, B.M. Fu, S. Haque, M. He, Y.J. Hu, C. Kambhamettu, H. Kangarloo, S.Y. Le, M.G. Mini, Y. Mun, M. Musavi, U. Sinha, T. Thomas, H. Valafar, proceedings of the International Conference on Mathematic and Engineering Techniques in Medicine and Biological Sciences (METMBS), Las Vegas, NV, Vol. 11, CSREA Press, June 24-27, 2002. B.D. French, C. Domnisoru, H. Ressom and M.T. Musavi, "Confidence value prediction of called genetic bases using a fuzzy predication system," Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '02), CSREA Press, ISBN 1-892512-39-4, H.R. Arabnia (Ed.), pp. 203-209, Las Vegas, NV, June 24-27, 2002. Domnisoru, C., X. Zhan, and M.T. Musavi, "Cross-Talk Filtering in Four Dye Flourescence-based DNA Sequencing", Electrophoresis, Vol. 21, No. 14, pp. 2983-2989, August 2000. McNally, C., C. Domnisoru, M. T. Musavi, "Building a DNA Database to Compare the Accuracy of Base Calling," Proceedings of The 2002 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, METMBS'02: Las Vegas, USA, June 24-27, pp. 217-223, 2002.. Domnisoru, C., and M.T. Musavi, "Mobility Shift Modeling for DNA Sequencing Data," Proceedings of IASTED International Symposium Modelling and Simulation (MS'2001), Pittsburg, PA, May 16-18, 2001. Domnisoru, C., X. Zhan, and M.T. Musavi, "Cross-Talk Filtering in Four Dye Flourescence-based DNA Sequencing," Electrophoresis, Vol. 21, No. 14, pp. 2983-2989, August 2000. Domnisoru, C. and M. Musavi, "Basecalling Algorithm for DNA Electrophoresis Sequencing Data," Plenary presentation, 4th Annual Conference on Computational Genomics organized by The Institute for Genomic Research TIGR, Baltimore, MD, November 16-19, 2000. Domnisoru, C., Musavi, M. T., "Mechanical Shift Compensation for DNA Trace File Processing," Proceeding of the Third International Symposium on Capillary Electrophoresis and Related Microscale Techniques, Hong Kong, June 14-17, 2000. Domnisoru, C., Musavi, M. T., "Base Calling Algorithm for DNA Electrophoresis Sequencing," Proceedings of the Third International Symposium on Capillary Electrophoresis and Related Microscale Techniques, Hong Kong, June 14-17, 2000. Domnisoru, C., Musavi, M. T., "Adaptive Base Calling Strategy," Proceedings of the Third International Symposium on Capillary Electrophoresis and Related Microscale Techniques, Hong Kong, June 14-17, 2000. Domnisoru, D. and M.T. Musavi, "Filtering Technique for Fluorescene-Based DNA Sequencing Data," Proceedings of the 2000 IEEE Canadian Conference on Electrical and Computer Engineering (CCECE), CD, IEEE Catalog Number: 00TH8492C, ISBN: 0-7803-5958-5, pp. 498-503, Dalhousie University, Halifax, NS, Canada, May 9-12, 2000. Domnisoru, D. and M.T. Musavi, "Mechanical Shift and Base Spacing Modeling and Compensation for DNA Sequencing," Proceedings of the International Association of Science and Technology for Development (IASTED) Conference on Modeling and Simulation, IASTED/ACTA Press, Anaheim, ISBN: 0-88986-284-2, ISSN: 1021-8181, pp. 470-476, Pittsburgh, Pennsylvania, May 15-17, 2000. |
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