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

Friday, 14 June 2013 04:00Web

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 metho

**d.**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. |