R5412301 Computational Molecular Biology

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Code No: R5412301

IV B.Tech I Semester(R05) Regular/Supplementary Examinations, December 2009 COMPUTATIONAL MOLECULAR BIOLOGY (Bio-Technology) Time: 3 hours Max Marks: 80 Answer any FIVE Questions All Questions carry equal marks ????? 1. You do protein BLAST searches of the SWISS-PROT and the non- redundant databank using the same sequence as query, and you get the same top hits, however, the E-values for the top hit are different. Why could this happen. Explain. [16] 2. Write short notes on: (a) Relationship of multiple sequence alignment to Phylogenetic analysis (b) Uses of multiple sequence alignment.

[8+8]

3. (a) Describe various methods to achieve MSA. What experimental data can be used to evaluate them? (b) What problems are confronted in phylogenetic analyses? Discuss the ways to test phylogenies. [8+8] 4. (a) Explain how the likelihood of a tree is calculated in maximum likelihood analysis of DNA data. (b) Identify two advantages and two disadvantages of molecular phylogenetic methods.

[8+8]

5. What are the tools used to assemble the sequence in a genome.

[16]

6. How could you analysis the Micro array data.

[16]

7. Comment on the nature of information provided by structure classification of databases.

[16]

8. (a) What are the proteins which assist in protein folding? (b) Write their classification and function.

[8+8] ?????

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Code No: R5412301

IV B.Tech I Semester(R05) Regular/Supplementary Examinations, December 2009 COMPUTATIONAL MOLECULAR BIOLOGY (Bio-Technology) Time: 3 hours Max Marks: 80 Answer any FIVE Questions All Questions carry equal marks ????? 1. (a) What are the advantages and disadvantages of using sequence-to-sequence (SmithWaterman, BLAST etc) searches with the sequences and of using blocks-to- sequences searches. (b) What is the PSI-BLAST program? How does it work and how does it relate to other BLAST programs. [8+8] 2. (a) Describe the use of Scoring matrices and Gap penalties in Sequence alignment. (b) Write a note on Parametric sequence alignment?

[8+8]

3. Explain (a) Three ways that have been used to estimate the age of a node (b) How to use a fossil to date a node?

[8+8]

4. Explain the model that computes the distance from the determinant of the matrix of co-occurrence of nucleotides in the two species. [16] 5. Discuss in detil how positional cloning plays an important role in desease gene identification.

[16]

6. How micro array technology useful in comparative genomics.

[16]

7. What are the approaches used for identifing proteins coding regions?

[16]

8. What is Block substitution matrices (BLOSOM) Describe them in detail?

[16]

?????

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Code No: R5412301

IV B.Tech I Semester(R05) Regular/Supplementary Examinations, December 2009 COMPUTATIONAL MOLECULAR BIOLOGY (Bio-Technology) Time: 3 hours Max Marks: 80 Answer any FIVE Questions All Questions carry equal marks ????? 1. Explain : (a) What do the basic types of BLAST do (blastn, blastp, blastx, PSI-BLAST?) (b) BLAST: Parameters, computational procedure, and interpretation of output. [8+8] 2. Explain about the importance of Multiple sequence alignment and its applications? [16] 3. Explain (a) Three ways that have been used to estimate the age of a node (b) How to use a fossil to date a node?

[8+8]

4. Briefly justify the reasons for treating transversions and transitions differently in Kimura two parameter model. [16] 5. Explain parallel strategies to examine genes simultaneously.

[16]

6. How could you analysis the Micro array data.

[16]

7. Comment on the nature of information provided by structure classification of databases.

[16]

8. Describe the different databases available for storage of protein resources.

[16]

?????

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Code No: R5412301

IV B.Tech I Semester(R05) Regular/Supplementary Examinations, December 2009 COMPUTATIONAL MOLECULAR BIOLOGY (Bio-Technology) Time: 3 hours Max Marks: 80 Answer any FIVE Questions All Questions carry equal marks ????? 1. Explain. The iterative use of PSSM’s gives Psi-BLAST enhanced ability to detect remote homologs, relative to “ordinary” BLAST. [16] 2. (a) Why do we use dynamic programming algorithms for pair wise sequence alignment problems but not for multiple pairwise alignment? (b) Explain in a few words how Clustal W aligns sequences.

[8+8]

3. (a) What is a horizontal gene transfer (HGT)? (b) Briefly explain the role of guide trees in progressive multiple sequence alignment algorithms.[8+8] 4. Explain (a) What are some of the advantages of using molecular data to infer evolutionary relationships? (b) What is the chance of randomly picking the one rooted phylogenetic tree that describes the true relationship between a group of eight organisms? Are the odds better or worse for randomly picking among all possible unrooted trees for those organisms? Explain. [8+8] 5. Discuss in detil how positional cloning plays an important role in desease gene identification.

[16]

6. Write short notes: (a) Exon shuffling (b) Minimal gene set.

[8+8]

7. What are the approaches used for identifing proteins coding regions?

[16]

8. What is Block substitution matrices (BLOSOM) Describe them in detail?

[16]

?????