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Published on: November 6, 2016
Run probabilities of seed-like patterns and identifying good transition seeds
1Department of Mathematics, National University of Singapore, Singapore, Republic of Singapore.
Abstract:
Transition seeds exhibit a good tradeoff between sensitivity and specificity for homology search in both coding and non-coding regions. However, identifying good transition seeds is intractable. This work studies the hit probability of high-order seed patterns. Based on our theoretical results, we propose an efficient method for ranking transition seeds for seed design and list good seeds in different Bernoulli sequence models.
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