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Title: In search of good predictors for identifying effective spaced seeds in homology search
Keywords: homology search, spaced seed, sensitivity, hitting probability, predictor, seed filter, sampling trick
Issue Date: 23-Aug-2005
Citation: LI JIANWEI (2005-08-23). In search of good predictors for identifying effective spaced seeds in homology search. ScholarBank@NUS Repository.
Abstract: It has been observed that the spaced seeds have better speed and sensitivity than the consecutive seeds with the same weight. Different spaced seeds have different sensitivities. To find the effective spaced seed in the sense of sensitivity is a very computationally challenging problem. For short spaced seeds, one can obtain the effective seeds by exhaustive search. However, this is impractical for long spaced seeds. We propose predictors to reduce the computation to identify the effective spaced seed which can be computed very quickly and predict well. We also introduce some index variable to filter the spaced seeds, with which we only need to handle very few seeds but can obtain the effective seeds in a good speed. For even longer seeds, we introduce a sampling trick. Combined with the method of predictors and filters, we can find effective seeds as fast as before.
Appears in Collections:Master's Theses (Open)

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