FCH 532 Homework 4
This assignment is due Monday in class!
Put your name and student ID number on the top of each page.
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1. (a) Using the PAM-250 log odds substitution matrix and the Needleman-Wunsch
algorithm, find the best alignment of the two peptides PQRSTV and PDLRSCPSV.
P
Q
R
S
T
V
P
6
0
0
1
0
-1
D
-1
2
-1
0
0
2
L
-3
-2
-3
-3
-2
2
R
0
1
6
0
-1
-2
S
1
-1
0
2
1
-1
C
-3
-5
-4
0
-2
-2
P
6
0
0
1
0
-1
S
1
-1
0
2
1
-1
V
-1
-2
-2
-1
0
4
First, transform the matrix and then determine the best alignment
P
D
L
R
S
C
P
S
V
P
6
-1
-3
0
1
-3
6
1
-1
Q
0
2
-2
1
-1
-5
0
-1
-2
R
0
-1
-3
6
0
-4
0
0
-2
S
1
0
-3
0
2
0
1
2
-1
T
0
0
-2
-1
1
-2
0
1
0
V
-1
2
2
-2
-1
-2
-1
-1
4
(b) What is its alignment score using a gap penalty of -8 for opening a gap and -2 for
every “residue” in the gap?
(c) What is its normalized alignment score (NAS) using the scoring system of 10 for each
identity, 20 for each identity involving Cys, and -25 for every gap?
(d) Is this NAS indicative of a homology? Explain.
2. You have been given an unknown protein to identify. You digest it with trypsin and,
by using Edman degradation, find that one of the resulting peptide fragments has the
sequence GIIWGEDTLMEYLENPK.
Using BLAST, find the most probably identity (or identities) of the unknown protein.
To carry out a search on the BLAST server, go to http://www.ncbi.nlm.nigh.gov/blast/
and, under “Protein BLAST,” click on the link “standard protein-protein BLAST
[blastp]” for comparing an amino acid query sequence against a protein sequence
database. In the window that comes up, enter the above sequence (without spaces or
punctuation) into the sequence box, from the “Choose database” pulldown menu select
“nr,” and click on the BLAST button.
3. You have manufactured a DNA chip consisting of 4 rows and 10 columns in which the
Mth column contains DNAs of the sequence 5’-GACCTGACGT-3’ but with a different
base in the Mth position for each of the 4 rows (from top to bottom, G, A, T, and C).
Draw the appearance of the chip after it is hybridized with fluorescently labeled RNA of
sequence (a) 5’-ACGUCAGGUC-3’ and (b) 5’-ACGUCUGGUC-3’
4. Describe in detail dideoxy sequencing (Sanger Method). How does this work?
5. Outline chemical synthesis of a chemical oligonucleotide.