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BINC 2017 - Part 2 questions
A question paper containing 55 questions (10 pages) is provided. A separate answer sheet (30 pages) to answer 20 questions is given. Each 10 mark answer needs to be written on one side of a page only. Each question is of 10 marks. The marks subdivisions are: 5+5, 6+4, 7+3, 4+3+3, 10.

Bioinformatics :
1. What is Molecular dynamic simulation. How is temperature increased.
2. Draw Ramachandran plot. Allowed and disallowed regions.
3. Ramachandran plot. Steric hindrance and angles.
4. Amino acids- polar, non-polar, hydrophobic, hydrophilic, aromatic, positive, negative. Why are there some exceptions.
5. QSAR. Pharmacophore model.
6. Docking- rigid flexible semi-flexible. Ligand based drug designing.
7. Monte carlo docking. Structure based drug design.
8. Array express DB. Synonymous SNP vs non synonymous. Role in evolution.
9. Protein threading method.
10. Artificial neural networks. Higher orders (BRNN). Use in secondary structure prediction.
11. Supervised vs unsupervised learning with example.
12. 2d page numerical
13. Fastq format. Something else
14. Flux balance analysis.
15. Rnaseq vs dnaseq.
16. KEGG database. Something else
17. Numerical on dna microarray
18. Numerical on gene expression
19. Denovo assembly
20. Boolean network simulation
21. Leonard jones potential numerical
22. Force field calculation due to torsion angles numerical
23. Gene regulatory networks.

Biology :
1. Competitive vs non competitive inhibition with diagram and LB plot.
2. Promoter, enhancer, locus region.
3. Operon model. Gene expression
4. Mitochondrial dna related to maternal inheritance.
5. Isozymes. Examples. Something else.

6. Dissociation constant numerical
7. Bohrs radius numerical
8. Calculate ph.
9. Endergonic vs exergonic reaction. Relation with free energy.

11. Fluorescence numerical
12. Enzyme kinetics numerical

Information Technology :
1. NoSQL merits demerits. GET POST methods in CGI.
2. Pseudocode of adding 2 n*n matrices, the sum of rows and columns of resultant matrix.
3. Program to input 3 words. Calculate vowels and consonants. Toggle upper case lower case. Replace all vowels with x.
4. Program : Result file is provided. 3 columns are : name, roll no, marks. Take marks column. Find the highest and lowest marks. Find average marks.
5. Create table. Perform some operations. Bubble sort algorithm.

Maths :
6. Solve 2nd order linear differential equation.
7. Matrix ‘A’ and inverse matrix given. Find value of : A^2 + 2A + ....
8. Calculate mean and variance of first n natural numbers. Population variance and...
9. Vector numerical.
10. Eigen vector calculation.

Statistics :
11. Binomial distribution numerical
12. Poisson distribution numerical
13. Null hypothesis numerical
14. Markov chain numerical
15. Testing of hypothesis numerical

PAPER 3 - Programming

1a. Intra Molecular Distance Matrix calculation (50 marks) : ATOM lines (155) of a pdb file are provided in input file (only C@ residues). Calculate intra molecular distance between each C@ residue. If distance >= 6, print 1 in distance matrix of output file, else print 0 in distance matrix. Comment on the secondary structures present.

1b. Chou fasman prediction (50 marks) : Amino acid sequence (50 residues) is provided in input file. Extract it. Make octamers of amino acids from the file and calculate their alpha and beta propensity by using second input file. Eg. - 1-8, 2-9, 3-10,....till 50. Second input file contains 20 amino acids with their alpha and beta propensity values in 3 columns. Parse through it using array or store it in a hash. Print the resultant alpha, beta propensity scores for each octamer in output file.


2a. Distance calculation (60 marks) : ATOM lines of a pdb file are provided in input file. Calculate distance between backbone amino acid and side chains. Many other questions were also there.

2b. Gene silencing (40 marks) : mRNA sequence is provided in first input file. miRNA sequences(3) are provided in second input file. Find when gene silencing will occur.
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