Northeastern University COM3113 -- Assignments

COM3113 -- Fundamentals of Programming -- Assignments

College of Computer Science -- Northeastern University

Fall Quarter 2001

Lab Session 2

Oct. 9th

Lab Task

The lab consists of two parts.

The first part:

Convert a DNA sequence into protein sequence according to the following genetic table.

Second Position of Codon

F
i
r
s
t

P
o
s
i
t
i
o
n

TTT	Phe	[F]
TTC	Phe	[F]
TTA	Leu	[L]
TTG	Leu	[L]

TCT	Ser	[S]
TCC	Ser	[S]
TCA	Ser	[S]
TCG	Ser	[S]

TAT	Tyr	[Y]
TAC	Tyr	[Y]
TAA	Ter	[end]
TAG	Ter	[end]

TGT	Cys	[C]
TGC	Cys	[C]
TGA	Ter	[end]
TGG	Trp	[W]

T
h
i
r
d

P
o
s
i
t
i
o
n

CTT	Leu	[L]
CTC	Leu	[L]
CTA	Leu	[L]
CTG	Leu	[L]

CCT	Pro	[P]
CCC	Pro	[P]
CCA	Pro	[P]
CCG	Pro	[P]

CAT	His	[H]
CAC	His	[H]
CAA	Gln	[Q]
CAG	Gln	[Q]

CGT	Arg	[R]
CGC	Arg	[R]
CGA	Arg	[R]
CGG	Arg	[R]

ATT	Ile	[I]
ATC	Ile	[I]
ATA	Ile	[I]
ATG	Met	[M]

ACT	Thr	[T]
ACC	Thr	[T]
ACA	Thr	[T]
ACG	Thr	[T]

AAT	Asn	[N]
AAC	Asn	[N]
AAA	Lys	[K]
AAG	Lys	[K]

AGT	Ser	[S]
AGC	Ser	[S]
AGA	Arg	[R]
AGG	Arg	[R]

GTT	Val	[V]
GTC	Val	[V]
GTA	Val	[V]
GTG	Val	[V]

GCT	Ala	[A]
GCC	Ala	[A]
GCA	Ala	[A]
GCG	Ala	[A]

GAT	Asp	[D]
GAC	Asp	[D]
GAA	Glu	[E]
GAG	Glu	[E]

GGT	Gly	[G]
GGC	Gly	[G]
GGA	Gly	[G]
GGG	Gly	[G]

Details:

You can hard-coded a DNA string in your program.
Translate the sequence in forward direction.
Begin with the very first character in the sequence.
Print out your protein sequence into screen.
Although you hard-code the DNA sequence into your program, your code should be correct for any given DNA sequence. I mean when I test your code, I will change the content of your DNA sequence.
For more method of String, you can go tohttp://java.sun.com/j2se/1.3/docs/api/java/lang/String.html

Second Part

According to the following hydrophobicity table, find out the highest-scoring segment in the protein sequence that you get in part 1. 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.

Requirements:

If you can finish the lab at the end of this session, please hand in your source code both in hardcopies and in email formate.

The deadline for this lab assignment is the end of next Monday, Oct. 15th.

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