Write a program to compute the optimal sequence alignment of two DNA strings. This program will introduce you to the emerging field of computational biology in which computers are used to do research on biological systems. Further, you will be introduced to a powerful algorithmic design paradigm known as dynamic programming.

Biology review.  A genetic sequence is a string formed from a four-letter alphabet {Adenine (A), Thymine (T), Guanine (G), Cytosine (C)} of biological macromolecules referred to together as the DNA bases. A gene is a genetic sequence that contains the information needed to construct a protein. All of your genes taken together are referred to as the human genome, a blueprint for the parts needed to construct the proteins that form your cells. Each new cell produced by your body receives a copy of the genome. This copying process, as well as natural wear and tear, introduces a small number of changes into the sequences of many genes. Among the most common changes are the substitution of one base for another and the deletion of a substring of bases; such changes are generally referred to as point mutations. As a result of these point mutations, the same gene sequenced from closely related organisms will have slight differences.

The problem.  Through your research you have found the following sequence of a gene in a previously unstudied organism.

A A C A G T T A C C

What is the function of the protein that this gene encodes? You could begin a series of uninformed experiments in the lab to determine what role this gene plays. However, there is a good chance that it is a variant of a known gene in a previously studied organism. Since biologists and computer scientists have laboriously determined (and published) the genetic sequence of many organisms (including humans), you would like to leverage this information to your advantage. We'll compare the above genetic sequence with one which has already been sequenced and whose function is well understood.

T A A G G T C A

Edit-distance.  In this assignment we will measure the similarity of two genetic sequences by their edit distance, a concept first introduced in the context of coding theory, but which is now widely used in spell checking, speech recognition, plagiarism detection, file revisioning, and computational linguistics. We align the two sequences, but we are permitted to insert gaps in either sequence (e.g., to make them have the same length). We pay a penalty for each gap that we insert and also for each pair of characters that mismatch in the final alignment. Intuitively, these penalties model the relative likeliness of point mutations arising from deletion/insertion and substitution. We produce a numerical score according to the following table, which is widely used in biological applications:

operation	cost
insert a gap	2
align two characters that mismatch	1
align two characters that match	0

Here are two possible alignments of the strings x = "AACAGTTACC" and y = "TAAGGTCA":

x y cost ------------ A T 1 A A 0 C A 1 A G 1 G G 0 T T 0 T C 1 A A 0 C - 2 C - 2 --- 8

x y cost ------------ A T 1 A A 0 C - 2 A A 0 G G 0 T G 1 T T 0 A - 2 C C 0 C A 1 --- 7

The first alignment has a score of 8, while the second one has a score of 7. The edit-distance is the score of the best possible alignment between the two genetic sequences over all possible alignments. In this example, the second alignment is in fact optimal, so the edit-distance between the two strings is 7. Computing the edit-distance is a nontrivial computational problem because we must find the best alignment among exponentially many possibilities. For example, if both strings are 100 characters long, then there are more than 10^75 possible alignments.

We will explain a recursive solution which is an elegant approach. However it is far too inefficient because it recalculates each subproblem over and over. Once we have defined the recursive definition we can redefine the solution using a dynamic programming approach which calculates each subproblem once.

A recursive solution.  We will calculate the edit-distance between the two original strings x and y by solving many edit-distance problems on the suffixes of the two strings. We use the notation x[i] to refer to character i of the string. We also use the notation x[i..M] to refer to the suffix of x consisting of the characters x[i], x[i+1], ..., x[M-1]. Finally, we use the notation opt[i][j] to denote the edit distance of x[i..M] and y[j..N]. For example, consider the two strings x = "AACAGTTACC" and y = "TAAGGTCA" of length M = 10 and N = 8, respectively. Then, x[2] is 'C', x[2..M] is "CAGTTACC", and y[8..N] is the empty string. The edit distance of x and y is opt[0][0].

Now we describe a recursive scheme for computing the edit distance of x[i..M] and y[j..N]. Consider the first pair of characters in an optimal alignment of x[i..M] with y[j..N]. There are three possibilities:

1. The optimal alignment matches x[i] up with y[j]. In this case, we pay a penalty of either 0 or 1, depending on whether x[i] equals y[j], plus we still need to align x[i+1..M] with y[j+1..N]. What is the best way to do this? This subproblem is exactly the same as the original sequence alignment problem, except that the two inputs are each suffixes of the original inputs. Using our notation, this quantity is opt[i+1][j+1].

2. The optimal alignment matches the x[i] up with a gap. In this case, we pay a penalty of 2 for a gap and still need to align x[i+1..M] with y[j..N]. This subproblem is identical to the original sequence alignment problem, except that the first input is a proper suffix of the original input.

3. The optimal alignment matches the y[j] up with a gap. In this case, we pay a penalty of 2 for a gap and still need to align x[i..M] with y[j+1..N]. This subproblem is identical to the original sequence alignment problem, except that the second input is a proper suffix of the original input.

opt[i][j] = min { opt[i+1][j+1] + 0/1, opt[i+1][j] + 2, opt[i][j+1] + 2 }

A dynamic programming approach.  A direct implementation of the above recursive scheme will work, but it is spectacularly inefficient. If both input strings have N characters, then the number of recursive calls will exceed 2^N. To overcome this performance bug, we use dynamic programming. (Read the first section of Section 9.6 for an introduction to this technique.) Dynamic programming is a powerful algorithmic paradigm, first introduced by Bellman in the context of operations research, and then applied to the alignment of biological sequences by Needleman and Wunsch. Dynamic programming now plays the leading role in many computational problems, including control theory, financial engineering, and bioinformatics, including BLAST (the sequence alignment program almost universally used by molecular biologist in their experimental work). The key idea of dynamic programming is to break up a large computational problem into smaller subproblems, store the answers to those smaller subproblems, and, eventually, use the stored answers to solve the original problem. This avoids recomputing the same quantity over and over again. Instead of using recursion, use a nested loop that calculates opt[i][j] in the right order so that opt[i+1][j+1], opt[i+1][j], and opt[i][j+1] are all computed before we try to compute opt[i][j].

Recovering the alignment itself.  The above procedure describes how to compute the edit distance between two strings. We now outline how to recover the optimal alignment itself. The key idea is to retrace the steps of the dynamic programming algorithm backwards, re-discovering the path of choices (highlighted in red in the table above) from opt[0][0] to opt[M][N]. To determine the choice that led to opt[i][j], we consider the three possibilities:

1. The optimal alignment matches x[i] up with y[j]. In this case, we must have opt[i][j] = opt[i+1][j+1] if x[i] equals y[j], or opt[i][j] = opt[i+1][j+1] + 1 otherwise.

2. The optimal alignment matches x[i] up with a gap. In this case, we must have opt[i][j] = opt[i+1][j] + 2.

3. The optimal alignment matches y[j] up with a gap. In this case, we must have opt[i][j] = opt[i][j+1] + 2.

 x   y  cost
------------
 A   T   1
 A   A   0
 C   -   2
 A   A   0
 G   G   0
 T   G   1
 T   T   0
 A   -   2
 C   C   0
 C   A   1

API specification. Your program EditDistance.java must be organized as a library of static methods with the following API:

public class EditDistance
--------------------------------------------------------------------------------
int penalty(char a, char b)     // return the penalty for aligning char a and char b

int min(int a, int b, int c)    // return the min of 3 integers

void main(String[] args)        // read 2 strings from standard input.
                                // compute and print the edit distance between them.
                                // output an optimal alignment and associated penalties.
                               

Your program. Write a program EditDistance.java that reads, from standard input, two strings of characters. (Although, in the application described, the characters represent genetic sequences, your program should handle any sequence of alphanumeric characters.) Your program should then compute and print the edit distance between the two strings. Finally, it should recover the optimal alignment and print it out along with the individual penalties, using the following format:

• The first line should contain the edit distance, preceded by the text "Edit distance = ".

• Each subsequent line should contain a character from the first string, followed by the paired character from the second string, followed by the associated penalty. Use the character '-' to indicate a gap in either string.

                             % java EditDistance < example10.txt
                             Edit distance = 7
                             A T 1
                             A A 0
                             C - 2
                             A A 0
                             G G 0
                             T G 1
                             T T 0
                             A - 2
                             C C 0
                             C A 1

The subdirectory sequence from the COS126 ftp site contains short test data files and actual genomic data files, as well as the readme.txt for this assignment. You also can download a .zip of the whole directory. Be sure to test thoroughly using the short test files and the longer actual data files. Also, make up a short test file of your own and describe it in your readme.txt file.

Analysis.  After you have tested your program using not only the example provided above, but also the many short test data files in the sequence subdirectory, it is time to analyze its running time and memory usage. Using the genomic data sets referred to in the readme.txt file, use a doubling hypothesis to estimate the running time (in seconds) of your program as a function of the lengths of the two input strings M and N. For simplicity, assume M = N in your analysis. Also analyze the memory usage (in bytes). Be sure to enter these results in your readme and answer all the questions.

Submission.   Submit the files: EditDistance.java and readme.txt.