COM3113 -- Fundamentals of Programming -- Assignments
College of Computer Science -- Northeastern University
Fall Quarter 2002
Assignment 6
Due by the end of Dec. 3
Problem Description:
According to the following hydrophobicity table, find out the highest-scoring segment in the protein sequence. Suppose every window consists of 3 amino acids. Compute all of the possible scores and find out the highest one.
Four hydrophobicity related amino acid indices.
| amino acid |
Kyte & |
Bull & |
Radzicka & |
Eisenberg & |
| |
Doolittle |
Breese |
Wolfenden |
McLachlan |
| I |
4.5 |
-2.26 |
1.31 |
0.99 |
| V |
4.2 |
-1.56 |
1.09 |
0.84 |
| L |
3.8 |
-2.46 |
1.21 |
0.89 |
| F |
2.8 |
-2.33 |
1.27 |
0.92 |
| C |
2.5 |
-0.45 |
1.36 |
0.76 |
| M |
1.9 |
-1.47 |
1.27 |
0.94 |
| A |
1.8 |
-0.20 |
-0.06 |
0 (n/a) |
| G |
-0.4 |
0.00 |
-0.41 |
0 (n/a) |
| T |
-0.7 |
-0.52 |
-0.27 |
0.09 |
| S |
-0.8 |
-0.39 |
-0.50 |
-0.67 |
| W |
-0.9 |
-2.01 |
0.88 |
0.67 |
| Y |
-1.3 |
-2.24 |
0.33 |
-0.93 |
| P |
-1.6 |
-0.98 |
0.00 |
0.22 |
| H |
-3.2 |
-0.12 |
0.49 |
-0.75 |
| Q |
-3.5 |
0.16 |
-0.73 |
-1.00 |
| N |
-3.5 |
0.08 |
-0.48 |
-0.86 |
| E |
-3.5 |
-0.30 |
-0.77 |
-0.89 |
| D |
-3.5 |
-0.20 |
-0.80 |
-0.98 |
| K |
-3.9 |
-0.35 |
-1.18 |
-0.99 |
| R |
-4.5 |
-0.12 |
-0.84 |
-0.96 |
Details
- Since each window consists of 3 amino acid, there are three possibilities for each protein sequence: one beginning with the very first amino acid in the sequence, one beginning with the second and one beginning with the third amino acid. You need to compute scores for all of these possible windows and find the biggest one.
- Use the second column in the above hydrophobicity score table. That is the Kyte & Doolittle value.
- Please use Java Applet in this assignment, similiar design as in your last assignment.
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