DOEACC Society 2006 DOEACC B Level BE7 Applied Bio-Informatics ( ) - Question Paper

BE7-R3: APPLIED BIOINFORMATICS
NOTE:
Time: three Hours Total Marks: 100
1.
a) describe the terms “Transcription” and “Translation” in the situation of protein synthesis.
b) Consider of DNA string 5’ ATCCACGGCCATAGG 3’. Write all the 5’ substrings ending
with G.
c) Write down the consensus sequence for the subsequent multiple alignment:
t g g t a t a c
t t g t t g a c
t g g a a g a t
t g c t a g a c
t g c t c c a c
t t c t c a a t
t g c a a g a g
t g c t a g a c
d) Why is dynamic programming technique not suitable for large-scale database homology
search?
e) What kinds of errors do occur in DNA fragment assembly problem?
f) Does degree of dependence relate to order of a Markov Chain? Briefly discuss.
g) What do you understand by the term “hidden” in a “hidden Markov model”?
(7x4)
2.
a) List the advantages of using Bioinformatics tools and techniques in analysing raw
sequence data.
b) The restriction enzymes EcoRI precisely recognise the site GAATTC and cut the E.coli
DNA into 2 fragments. Cuts are ranging from the 1st G and the 2nd A. Consider the
DNA sequence ATCCGAATTCATTG
Write down the resulting fragment cut by the above-mentioned enzyme.
c) discuss a typical GenBank record and define its main features.
(8+6+4)
3.
a) provide the basic dynamic programming algorithm for a pair-wise sequence alignment
problem.
b) Compare the contrast the gene structure of a prokaryote and eukaryote.
c) How is Genome learned at various levels? Briefly explain about the Human Genome
project.
(6+6+6)
4.
a) Consider the issue of aligning 2 tRNA sequence of E.coli. These sequences are
GGTGATTAGCT and GCTGATATAGCT. Derive a Global likeness alignment for the
above 2 sequences using the scoring scheme S(a,a)=+1;s(a,b)=-1 if a¹b; and gap=2.
BE7-R3 Page one of two January, 2006
1. ans ques. one and any 4 ques. from two to 7.
2. Parts of the identical ques. should be answered together and in the identical
sequence.
b) Using dynamic programming method, explain the algorithmic complexity of pairwise
alignment issue. Why is such technique not preferred for multiple alignment
sequence problem?
(12+6)
5.
a) describe a linear and affine gap penalty.
b) discuss the relevance and utility of multiple aligned sequences.
c) Which method is employed in popular “ClustalW” multiple alignment programs?
(4+4+10)
6.
a) Write a short note on PAM and Blosum scoring matrices.
b) How are homologous DNA sequences from the database retrieved using a typical
BLASTN program for a provided query nucleotide sequence?
c) How is PSI-BLAST various from BLASTN?
(4+10+4)
7.
a) describe the term “memoryless property” and “time homogeniety” property in connection
with the Markov Chains.
b) Consider the subsequent transition probability matrix. Identify the probable state, which is
likely to be visited more often from the initial state “A”? obtain out the fault in the last row
of this transition probability matrix.
\ A C G T
A 0.2 0.1 0.6 0.1
C 0.1 0.7 0.1 0.1
G 0.2 0.2 0.5 0.1
T 0.1 0.3 0.2 0.5
c) For a biological important functional site the transition probability matrices for “+” model
and “-“ model are provided beneath. Using these models suggest prediction methodology.
+ A C G T - A C G T
A 0.2 0.2 0.4 0.2 A 0.3 0.1 0.1 0.5
C 0.1 0.3 0.2 0.4 C
0.3
0.3
0.1
0.3
G 0.2 0.3 0.3 0.1 G 0.2 0.2 0.3 0.3
T 0.1 0.4 0.3 0.2 T 0.1 0.2 0.2 0.2
(4+4+10)
BE7-R3 Page two of two January, 2006

Earning:   Approval pending.