最优搜索机制下寻找最优插入-删除种子

空位种子极大地提高了生物分子序列比对的灵敏度,但不适合大量存在插入和删除字符的序列.在空位种子的基础上,提出了带插入-删除的生物序列比对种子,进一步提高了生物序列比对的效率.实验表明,采用最优搜索算法可以有效地在给定约束条件下寻找到最优的插入-删除种子,并且插入-删除种子比同长度的最优空位种子具有更高的生物序列比对敏感...

Finding Optimal Indel Seeds under Optimal Search Mechanism

Spaced seeds greatly improve the sensitivity of bio-sequences alignment, but they are not applicable for the sequences containing many insertions and deletions．Based on spaced seeds, we propose seeds with insertions and deletions (Indel seeds), which improves the sequences alignment sensitivity more. Experiments show that adopting optimal search algorithm can find optimal indel seeds under given constraints, further more, indel seeds have higher bio-sequences alignment sensitivity than that of spaced seeds.