LOYOLA COLLEGE (AUTONOMOUS), CHENNAI – 600 034  B.Sc. DEGREE EXAMINATION – PLANT BIOLOGY & BIOTECHNOLOGY

AE 09

FIFTH SEMESTER – NOV 2006

         PB 5404 – BIO-INFORMATICS

 

 

Date & Time : 06-11-2006/9.00-12.00         Dept. No.                                                       Max. : 100 Marks

 

 

PART A

 

Answer all the questions                                                                              (20 marks)

 

I      Choose the correct answer                                                                  (5 x1  = 5)

 

 

1. _________ is a secondary database.
2. a) PIR b) swissprot            c) prosite                          d) ncbi
3. _________ is a nucleic acid seqeuence database.
4. a) DDBK b) Genbank            c) sopma   d)PDB
5. _________ is the visual comparison of 2 sequences.
6. a) dotplot b) PDB   c) Lalign         d) blast
7. _________is a database search tool.
8. a) blast b) PIR          c) PDB       d) expasy.
9. ________is the software to find gene locations in genomes.
10. a) mapviewer b)  blast         c) fasta             d) sopma

 

 

II State True or False                                                                                    (5 x 1  =5)

 

6. GC % is related to Tm.
7. Proteases are enzymes which cut DNA sequences.
8. Rasmol is a protein structure database.
9. Protein structures can be downloaded from swissprot.
10. Swissmodel results can be obtained through email.

 

III  Complete the following                                                                (5 x 1 = 5)

 

11. _________is a Secondary structure prediction tool.
12. _________ is used to search NCBI protein sequence databases.
13. _________ is a protein structure visualization tool.
14. _________is a gene prediction software.
15. Tm represents _________ of DNA. .

 

 

 

 

IV Define the following                                                          .             (5 x  1 = 5)

 

16. Define : Transition
17. Expand PAM.
18. What is a Dendogram.
19. Expand : NCBI.
20. Expand : EMBL..

PART B

 

 

Answer any Five of the following , each in about 350 words.                 (5 x 8 =40)

 

21. Explain dotplot and its applications.
22. Explain promoter 2.0 and its applications.
23. Explain any 5 commands in rasmol.
24. Describe in general the various types of biological databases.
25. Explain peptide cutter and its applications.
26. Explain the software to identify the restriction site in DNA.
27. Explain SOPMA in detail.
28. Explain prosite patterns.

PART C

 

 

 

Answer  the following, each  in about 1500 words.          (2 x 20 = 40)

Draw diagrams / flowcharts wherever necessary.

 

 

 

29.a) Explain smithwaterman algorithm in detail.

Or

1. b) Discuss homology modelling in detail.

 

 

30.a) Discuss BLAST, its types, process and output format.

Or

1. b) Explain genbank and its file format.

 

 

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