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Question 4. (5 points) Longest common subsequence problem Suppose that you have a very fast machine to execute the Smith-Waterman algorithm with any user-specific substitution cost matrix and linear gap penalty (such special-purpose machines exist and were fashionable in the 90's). How would you use it to solve the longest common subsequence: Given two DNA sequences S and T, find the longest sequence X that is a subsequence of both S and T. Note: Subsequences and substrings are two different things. A subsequence is made of characters that occur in the right order in the input spring, but not necessarily consecutively. A substring is a set of consecutive characters of the input string. So every substring is a subsequence, but not vice- versa. For example, BOICS is a subsequence of BIOINFORMATICS, but it is not a substring. IRO is neither a subsequence nor a substring of BIOINFORMATICS.

          Question 4. (5 points) Longest common subsequence problem
Suppose that you have a very fast machine to execute the Smith-Waterman algorithm with any
user-specific substitution cost matrix and linear gap penalty (such special-purpose machines exist
and were fashionable in the 90's). How would you use it to solve the longest common
subsequence: Given two DNA sequences S and T, find the longest sequence X that is a
subsequence of both S and T.
Note: Subsequences and substrings are two different things. A subsequence is made of characters
that occur in the right order in the input spring, but not necessarily consecutively. A substring is a
set of consecutive characters of the input string. So every substring is a subsequence, but not vice-
versa. For example, BOICS is a subsequence of BIOINFORMATICS, but it is not a substring.
IRO is neither a subsequence nor a substring of BIOINFORMATICS.

Question 4. (5 points) Longest common subsequence problem
Suppose that you have a very fast machine to execute the Smith-Waterman algorithm with any
user-specific substitution cost matrix and linear gap penalty (such special-purpose machines exist
and were fashionable in the 90's). How would you use it to solve the longest common
subsequence: Given two DNA sequences S and T, find the longest sequence X that is a
subsequence of both S and T.
Note: Subsequences and substrings are two different things. A subsequence is made of characters
that occur in the right order in the input spring, but not necessarily consecutively. A substring is a
set of consecutive characters of the input string. So every substring is a subsequence, but not vice-
versa. For example, BOICS is a subsequence of BIOINFORMATICS, but it is not a substring.
IRO is neither a subsequence nor a substring of BIOINFORMATICS.

Added by Steven R.

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