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) How is Gene organisation is various in Eukaryotes compared to prokaryokes?
b) Why BLAST algorithm is heuristic?
c) How GenBank format is various from FastA format?
d) What is the edit distance of the words CCT and ACGCTT? Align the sequences ATT and
TTC.
e) Why higher order markov models are not generally used in Bioinformatics applications?
f) How can you obtain all open studying frames in a provided sequence?
g) Imagine you want to compute the shortest common super-sequence i.e. the shortest
sequence to which all sequences can be aligned without mismatches. Which cost/weight
scheme can you use? provide 1 example.
(7x4)
2.
a) Write the Needleman-Wunch algorithm for Global Alignment. Also mention the
changes necessary to solve local alignment issue.
b) elaborate 3 steps generally carried out for a typical fragment assembly algorithm?
Explain?
(10+8)
3.
a) What is biological motivation of sequence analysis?
b) presume you are provided a set of DNA sequence belonging to various species. What
strategy has to be adopted to obtain a common trend in these sequences?
c) elaborate the basic assumptions made while developing PAM and BLOSUM scoring
matrices?
(6+8+4)
4.
a) What do you mean by statistical significance? discuss the identical in the situation of BLAST
searches.
b) How PSI-BLAST and PHI-BLAST are various from BLAST?
c) Why low complexity sequences are masked in BLAST searches. Mention name of the
two programs used for this purpose.
(8+6+4)
5.
a) elaborate CG-islands? How will you proceed to obtain a predictive method for the identical
using 1st Order Markov Chain?
b) discuss the term “Staite transition probabilities” and “emmission probabilities” in the
situation of hidden Markov models.
c) explain the possible applications of Markov models in biological issues.
(8+4+6)
BE7-R3 Page one of two July, 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.
6.
a) What is homology-based approach for gene prediction?
b) What is DNA sequencing? explain DNA sequencing methodologies in brief.
(8+10)
7.
a) Let S1 = AATTCGCGTA and
S2 = TATCGCTACA
find the optimal global alignment using dynamic programming method. Use any
Scoring scheme of your option.
b) define the Viterbi algorithm used in hidden Markov model.
(10+8)
BE7-R3 Page two of two July, 2006

Earning:   Approval pending.