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
T C A G
F
i
r
s
t

P
o
s
i
t
i
o
n
T
TTTPhe[F]
TTCPhe[F]
TTALeu[L]
TTGLeu[L]
TCTSer[S]
TCCSer[S]
TCASer[S]
TCGSer[S]
TATTyr[Y]
TACTyr[Y]
TAATer[end]
TAGTer[end]
TGTCys[C]
TGCCys[C]
TGATer[end]
TGGTrp[W]
T
C
A
G
T
h
i
r
d

P
o
s
i
t
i
o
n
C
CTTLeu[L]
CTCLeu[L]
CTALeu[L]
CTGLeu[L]
CCTPro[P]
CCCPro[P]
CCAPro[P]
CCGPro[P]
CATHis[H]
CACHis[H]
CAAGln[Q]
CAGGln[Q]
CGTArg[R]
CGCArg[R]
CGAArg[R]
CGGArg[R]
T
C
A
G
A
ATTIle[I]
ATCIle[I]
ATAIle[I]
ATGMet[M]
ACTThr[T]
ACCThr[T]
ACAThr[T]
ACGThr[T]
AATAsn[N]
AACAsn[N]
AAALys[K]
AAGLys[K]
AGTSer[S]
AGCSer[S]
AGAArg[R]
AGGArg[R]
T
C
A
G
G
GTTVal[V]
GTCVal[V]
GTAVal[V]
GTGVal[V]
GCTAla[A]
GCCAla[A]
GCAAla[A]
GCGAla[A]
GATAsp[D]
GACAsp[D]
GAAGlu[E]
GAGGlu[E]
GGTGly[G]
GGCGly[G]
GGAGly[G]
GGGGly[G]
T
C
A
G

Details:

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

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.

Back to course index page