COMPUTATIONAL MOLECULAR BIOLOGY Question Papers (2008,Reg)

SET : 1

1. Ouline the steps in the BLAST algorithm.
2. a) Eplain why neither FASTA nor BLAST are guaranteed to return a sequence that has maximum similarity score with respect to the query sequence. b) Explain why hueristic programs such as FASTA or BLASTA are used for database searching instead of comparing the query sequence with the database sequences using dynamic programming.
3. a) What are the differences and similarities between cladograms, rooted and, unrooted phylograms. what information each tree conveys. b) Describe the 3 methods for constructing phylogenies: Maximum likelyhood, Neighbour Joining, and Maximum Parsimony.
4. Explain in detail about the symmetric model of DNA evolution.
5. What are the advantages of phylogenetic analysis .
6. Explain why every genome is different.
7. How many chain conformations are described by Ramachandran Plot?
8. What are the difficulties faced from ab initio protein structure prediction. How can we solve it.
   

SET : 2

1. a) What are the major extensions of BLAST? b) Discuss the areas of application of these programs.
2. Name some situations in which a molecular biologist wishes to perform a pair wise sequence alignment, multiple sequence alignment and sequence database searching. b) Briefly describe how the PAM and BLOSUM scoring matrices are derived and how they are different.
3. Write short jnotes on : a) Searching tree space b) Distance correction.
4. a) What are DNA substitution models? Expalin. b) What are DNA substitution models good for? Discuss.
5. What are the methods used to studying gene expression?
6. Describe the comparitive genomics of bacteria.
7. Protein structures are more highly conserved than sequences than sequences. Explain.
8. Transmembrane proteins are important in drug discovery. What are their properties and how can we generate their 3-D structures.

SET : 3

1. Explain the steps used by the BLAST algorithm and mention blast related programs.
2. a) Write about the significance of substitution scores and gap penalties in sequence alignment. b) Explain FASTA database similarity searching program.
3. Write short notes on : a) Rooted and Unrooted trees. b) Genes vs. species trees.
4. Explain about the strategy employed by Kimuras Two Parameter model in estimating substitution numbers.
5. Give a note on variety of polymorphic DNA markers and how they can be used for linkage studies.
6. Describe the organisation of nuclear DNA in eukaryotes.
7. Comment on the evolution of PDB. What are its classifications.
8. Explain the importance of protein designing in the field of drug designing.

SET : 4

1. Describe the following : a) General idea behind the PSI-BLAST approach. b) What problem does it solve (Input/Output)? HOw does it go about solving it?
2. What type of scoring matrix is used by FASTA? Explain about different substitution matrices?
3. Describe the following : a) Various tree building methods. b) Concept of Evolutionary trees.
4. Explain a) What is a change point, and how could you fetect it? b) What is the importance of the KA/KS ratio?
5. Write a short notes on : a) RFLP b) VNTRs c) STS d) EST
6. Discuss the application of microarray technology.
7. Write short notes : a) Protein sequence data b) Sequence data base search.
8. Describe the diffferent databases available for storage of protein resources.