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