[英语学习]生物信息课件_中科院_2.ppt

A sequence is a list of objects in some order. For example, (7, 21, 57) A sequence with k elements is a k-tuple. A sequence is different from a set in that repetition is allowed in the former but not in the later. DNAs and proteins are perfect examples of sequences with different alphabets. {G, A, T, C} for DNA {20 amino acids} for proteins. Sequence alignment is to check how well two or more sequences match with each other. Similarity means homology, ie, coming from a common source. “Nature is a tinkerer and not an inventor.” ---Jacob 1977 Global vs local alignment Global alignment - aaagcggaagtcacag ||.||.||||| |.|| aaggctgaagt-atag Local alignment - : aaagcggaagtcacag ......||||| .... aaggctgaagt-atag How many ways of intercalating two sequences of lengths n and m? Any pair-wise alignment can be transformed into an intercalated sequence. A completed alignment matrix Dynamic Programming Pros and Cons Advantages: Guaranteed in a mathematical sense to provide the optimal (very best or highest-scoring) alignment for a given set of scoringfunctions. Disadvantages: a) Slow due to the very large number of computational steps: O(n 2).b) Computer memory requirement also increases as the square of the sequence lengths. Therefore, it is difficult to use the method for very long sequences.  FASTA and BLAST FASTA - Idea - Problem of Dynamic Programming D.P. compute the score in a lot of useless area for optimal sequence FASTA focuses on diagonal area FASTA - Heuristic - Heuristic Good local alignment should have some exact match subsequence. FASTA - Hi Level Algorithm - Hi level algorithm Let q be a query max ? 0 For each sequence, s in DB compare q with s and compute a score, y if max y max ? y; bestSequence ? s ; Return bestSequence FASTA - Algorithm - Step 1 Find all hot-spots (matching words) // Hot spots are pairs of words of length k (k-tuple) that exa