Apostilas de Biologia Computacional  2009 - Lista 4, Notas de estudo de Biologia Computacional. Universidade Federal de Alagoas (UFAL)
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Apostilas de Biologia Computacional 2009 - Lista 4, Notas de estudo de Biologia Computacional. Universidade Federal de Alagoas (UFAL)

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Apostilas de Biologia Computacional da Universidade Estadual de Campinas, Primeiro Semestre de 2009, 4 Lista de Exercícios.
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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.

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