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This site is dedicated to algorithmic research in bioinformatics being carried out at National University of Singapore under Dr. Sung Wing Kin, Ken. Currently research is being done on microarray probe design, patter searching, genome annotation and protein structure prediction. Existing algorithms for microarray probe design usually select probes using the criteria of homogeneity, sensitivity, and specificity. Research is being done to include one additional criterion, uniformity, which further improves the quality of the probes selected. PatternHunter uses spaced seeds which is shown to be more sensitive and efficient than consecutive seed. This makes spaced seed a better choice than conventional consecutive seed for hit scanning in a BLAST-like approach. our work involves the study and design of multiple spaced seeds and we propose a novel approach that introduces gaps of various length into seeds. The gaps allow for variation in matching and thus increases the sensitivity.
Contact Information
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Send mail to
gunjanch@comp.nus.edu.sg with
questions or comments about this web site.
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