title: Run probabilities of seed-like patterns and identifying good transition seeds.
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.
authors.affiliation: Department of Mathematics, National University of Singapore, Singapore, Republic of Singapore.
authors.forename: Jialiang
authors.initials: J
authors.lastname: Yang
authors.forename: Louxin
authors.initials: L
authors.lastname: Zhang
mesh_terms: D016208:Databases, Factual; D015233:Models, Statistical; D010363:Pattern Recognition, Automated / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods