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MO640 – Biologia Computacional Primeiro Semestre de 2009 Quarta Lista de Exerćıcios
1. Given two sequences, which value is larger: their local similarity or their global similarity?
Why? How does their semi-global similarity compare with the other two values?
2. Show all optimal global alignments between sequences x = ACTGTGCT and y = ATGGTCT,
using match = +3, mismatch = −2, and gap = −5.
3. Longest Common Subsequence (LCS) Problem: given two sequence x and y, find the longest
subsequence present in both of them. A subsequence is a sequence that appears in the same
relative order, but not necessarily contiguous. For example, in the string abcdefg, “abc”, “abg”,
“bdf”, “aeg” are all subsequences. Use the Needleman-Wunsch algorithm to solve the LCS
problem. Justify your answer.
4. An alignment of circular strings is defined as an alignment of linear strings forming by cutting
(linearizing) these circular strings an arbitrary position. Devise an efficient algorithm to find an
optimal global alignment of circular strings.
5. A local alignment between two different strings x and y finds a pair of substrings, one in x
and the other in y, with maximum similarity. Suppose that we want to find a pair of (nonover-
lapping) substrings within string v with maximum similarity (Optimal Inexact Repeat problem).
Computing an optimal local alignment between v and v does not solve the problem, since the
resulting alignment may correspond to overlapping substrings. Devise an algorithm for the
Optimal Inexact Repeat problem.
6. A string x is called a supersequence of a string y if y is a subsequence of x. For example, ABLUE
is a supersequence for BLUE and ABLE. Given strings x and y, devise an efficient algorithm to
find the shortest supersequence for both x and y.