URGENT!!! Really need help with this. % Code to start Part 3 from. function HW7_

Question

URGENT!!! Really need help with this.

% Code to start Part 3 from.

function HW7_3

% Ask the user for DNA sequence 1.

prompt = 'Enter the first DNA sequence of length 1 to 99: ';

seq1 = input(prompt, 's');

len1 = length(seq1);

sprintf(' Seq 1 %s has %d bases', seq1, len1)

% Ask the user for DNA sequence 2.

prompt = 'Enter the second DNA sequence of length 1 to 99: ';

seq2 = input(prompt, 's');

len2 = length(seq2);

sprintf(' Seq 2 %s has %d bases', seq2, len2)

% Guess sequence 1 is longer than sequence 2.

longSeq = seq1;

longLen = len1;

shortSeq = seq2;

shortLen = len2;

% Correct an incorrect guess.

if (len2 > len1)

longSeq = seq2;

longLen = len2;

shortSeq = seq1;

shortLen = len1;

end

% Create "buffered" strings to facilitate the scan.

bufLength = longLen + 2 * shortLen;

scan1 = blanks(bufLength);

scan2 = blanks(bufLength);

% Fill the "scan" strings with dashes

for i = 1:bufLength

scan1(i) = '-';

scan2(i) = '-';

end

% Initialize the first scan string with the long sequence in the middle.

for i = shortLen + 1:shortLen + longLen

scan1(i) = longSeq(i-shortLen);

end

% Initialize the second scan string with the short sequence at the

% beginning.

for i = 1:shortLen

scan2(i) = shortSeq(i);

end

% Score & print the initial alignment.

score = scoreSequences(scan1, scan2);

printSeq(scan1, scan2, score);

% Rotate the short sequence to the right, score & print.

scan2 = rotateSeqRight(scan2);

score = scoreSequences(scan1, scan2);

printSeq(scan1, scan2, score);

% Repeat in a loop!!

end

% Use your scoring logic from part 1.

function score = scoreSequences(seq1, seq2)

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% Code to start Part 3 from.

function HW7_3

% Ask the user for DNA sequence 1.

prompt = 'Enter the first DNA sequence of length 1 to 99: ';

seq1 = input(prompt, 's');

len1 = length(seq1);

sprintf(' Seq 1 %s has %d bases', seq1, len1)

% Ask the user for DNA sequence 2.

prompt = 'Enter the second DNA sequence of length 1 to 99: ';

seq2 = input(prompt, 's');

len2 = length(seq2);

sprintf(' Seq 2 %s has %d bases', seq2, len2)

% Guess sequence 1 is longer than sequence 2.

longSeq = seq1;

longLen = len1;

shortSeq = seq2;

shortLen = len2;

% Correct an incorrect guess.

if (len2 > len1)

longSeq = seq2;

longLen = len2;

shortSeq = seq1;

shortLen = len1;

end

% Create "buffered" strings to facilitate the scan.

bufLength = longLen + 2 * shortLen;

scan1 = blanks(bufLength);

scan2 = blanks(bufLength);

% Fill the "scan" strings with dashes

for i = 1:bufLength

scan1(i) = '-';

scan2(i) = '-';

end

% Initialize the first scan string with the long sequence in the middle.

for i = shortLen + 1:shortLen + longLen

scan1(i) = longSeq(i-shortLen);

end

% Initialize the second scan string with the short sequence at the

% beginning.

for i = 1:shortLen

scan2(i) = shortSeq(i);

end

% Score & print the initial alignment.

score = scoreSequences(scan1, scan2);

printSeq(scan1, scan2, score);

% Rotate the short sequence to the right, score & print.

scan2 = rotateSeqRight(scan2);

score = scoreSequences(scan1, scan2);

printSeq(scan1, scan2, score);

% Repeat in a loop!!

end

% Use your scoring logic from part 1.

function score = scoreSequences(seq1, seq2)

Part 1: Create a Matlab script hw7_1.m that prompts the user for two DNA sequence strings and scores an alignment. Each A or T match contributes a value of +2 Each C or G match contributes a value of +3 Each mismatch or Gap contributes a score of -2 You can assume the input will be valid (only DNA bases) and the sequences will be at most 99 bases in length. For example, two sequences and their corresponding score would be Sequence 1ATGCTGACTGCA Sequence 2: CTTGAGACG- A/T score G/C score Mismatches + GAPS = 8*-2= -16 Score = 2* 2= +4 = 2* 3= +6 -6

Explanation / Answer

ackage com;
public class DList<T> {
private DNode<T> header, trailer;
private int size;
public DList() {
size = 0;
header = new DNode<T>(null, null, null);
trailer = new DNode<T>(null, header, null);
header.setNext(trailer);
}
// utility methods
public int size() {
return size;
}
public boolean isEmpty() {
return size == 0;
}
// give clients access to nodes, but not to the header or trailer
public DNode<T> getFirst() throws Exception {
if (isEmpty())
throw new Exception("Empty");
return header.getNext();
}
public DNode<T> getLast() throws Exception {
if (isEmpty())
throw new Exception("Empty");
return trailer.getPrev();
}
public DNode<T> getNext(DNode<T> v) throws Exception {
DNode<T> ans = v.getNext();
if (ans == null || ans == trailer)
throw new Exception("No such node");
return ans;
}
public DNode<T> getPrev(DNode<T> v) throws Exception {
DNode<T> ans = v.getPrev();
if (ans == null || ans == header)
throw new Exception("No such node");
return ans;
}
// methods to change the list
public void addBefore(T d, DNode<T> v) {
DNode<T> u = v.getPrev();
DNode<T> x = new DNode<T>(d, u, v);
u.setNext(x);
v.setPrev(x);
size++;
}
public void addAfter(T d, DNode<T> v) {
DNode<T> w = v.getNext();
DNode<T> x = new DNode<T>(d, v, w);
v.setNext(x);
w.setPrev(x);
size++;
}
public void addFirst(T d) {
addAfter(d, header);
}
public void addLast(T d) {
addBefore(d, trailer);
}
public T remove(DNode<T> v) throws Exception {
if (v == header || v == trailer)
throw new Exception("Sentinel");
DNode<T> u = v.getPrev();
DNode<T> w = v.getNext();
w.setPrev(u);
u.setNext(w);
size--;
return v.getData();
}
// LinkedList testing methods:
public String toString() {
String ans = "";
DNode<T> n = header;
ans += "(H)<-->";
do {
n = n.getNext();
if (n == trailer)
ans += "(T)";
else
ans += (n.getData() + "<-->");
} while (n != trailer);
return ans;
}
}

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