University: West Bengal University of Technology
Course: B.sc
Subject :Computational Biology and Bioinformatics
Year of Question Paper : 2013
CS/B.Sc.(H)/MOLBIO/MICROBIO/BT/GENE/SEM-4/CBB-402/2012
2012
COMPUTATIONAL BIOLOGY &
BIOINFORMATICS
Time Allotted : 3 Hours Full Marks : 70
The figures in the margin indicate full marks.
Candidates are required to give their answers in their own words as
far as practicable.
GROUP – A
( Multiple Choice Type Questions )
1. Choose the correct alternatives for any ten of the following :
[Marks 10 × 1 = 10]
i) Each Gen Bank entry includes
a) a concise description of the sequence
b) the scientific name
c) taxonomy of the source organism
d) all of these.
ii) Methods to perform DNA or RNA sequencing include
a) chromosome walking
b) shotgun sequencing
c) chain termination method
d) all of these.
iii) Brookhaven .................. is a database of 3D
structures.
a) DDBJ b) PDB
c) Swiss Prot d) Uni Gene.
iv) Phylogenetic tree depends on
a) MSA b) BLAST c) Global alignment d) none of these.
v) Which of the following is not true about Swiss Prot ?
a) Highly curated
b) Highly cross-referenced
c) Non-redundant database
d) redundancy.
vi) The low complexity region among the following is
a) 'aaggtcctagtagtcga' b) 'aaaaaaaaa'
c) 'atttattaaagcgctgcat' d) 'nnnnnnna'.
vii) Dynamic programing is used to
a) develop the phylogenetic tree
b) detect the most suitable alignment
c) detect the conserved domain of different protein
d) none of these.
viii) Pairwise Sequence alignment is associated with
a) the Baum-Welch Algorithm
b) the Viterbi Algorithm
c) Needleman-Wunuch Algorithm
d) None of these.
ix) Blastx is a tool of
a) search protein database using a translated
nucleotide query
b) search nucleotide database using a translated
nucleotide query
c) search protein database using a protein query
d) search translated nucleotide database using a
protein query.
x) The E-value of an alignment
a) is the expected number of sequences that give the
same Z-score or better if the database is probed
with a random sequence
b) is expertise value of sequences that give the same
P-value
c) is probability value of an alignment having more
than these smilarities
d) none of these.
xi) Fasta algorithm uses
a) k-tuple values b) LSP values
c) complex values d) none of these.
xii) Gap penalty in sequence alignment is
a) the penalty score for umatch between later
b) the penalty score for umatch between two gaps
c) The penalty score for umatch between same
residues
d) the penalty score for giving a gap to get maximum
match interpreting as insertion. deletion and
mutation.
GROUP – B
( Short Answer Type Questions )
Answer any three of the following. [Marks 3 × 5 = 15]
2. What is Ramachandran plot ? Explain the utility of
Ramachandran plot to predict secondary structure.
3. How would you get the conserved domain and get the
phylogenetic relation of the prion protein of horse, human,
macaca mulatta and chimpanzee. What is Pubmed ? What is
the name of the database where you get the inheritable
disease of human ?
4. Explain the term 'GIR'. What is central dogma in biology ?
Give example of experimental and theoretical approaches for
proteomics.
5. Write short note on any one of the following :
a) MSA
b) The experimental approaches to genome sequence data.
6. What is substitution matrix ? In PAM-250 the 250 stands for
what ? Write down the difference of PAM250 and BIOSSM62
matrix.
GROUP – C
( Long Answer Type Questions )
Answer any three of the following. [Marks 3 × 15 = 45]
7. What are E-value and Z-value of an alignment ? Write down
the steps. Find a nucleotide from NCBI namely
Topoisomerase. Convert it to protein. Find the homologue of
the protein from the databases. Then find the similarity of
the corresponding protein with other species. What is pairwise
alignment and k-tuple ? Write the use of HSSP in Blast.
[Marks 2 + 2 + 6 + 2 + 3]
8. Explain the main features of CSD. Write the main features of
SCOP and CATH. Explain the information obtained from
PROPSEARCH method. [Marks 5 + 3 + 3 + 4]
9. Align the following two sequences by dynamic programming
method : 15
G A A T T C A G T T A ( sequence # 1 )
G G A T C G A ( sequence # 2 ).
10. Write down the name of the tools of NCBI where local
alignment is done. What is the algorithm behind the
program ? What are the applications of doing an MSA ? You
have beeen given a protein along with the sequence of it.
How would you identify the protein ? If not possible, then
how would you get an idea of the functionality of the
protein ? Give proper explanation. Define domain of a
protein. Write a short note on Blast's working procedure.
[Marks 1 + 1 + 2 + 3 + 1 + 2 + 2 + 1 + 2]
11. State the differences between homology and similarity.
Write down six emerging fields in bioinformatics. You have
given a sequence of African elephant and Indian elephant.
How would you draw the phylogenetic relation beween
them ? What result would you expect ? What is relative
mutability ? [Marks 3 + 3 + 4 + 2 + 3]
12. What is E-value and Z-value of an alignment ? Write down
the steps only. How will you show through bioinformatics
that the insulin sequence of HORSE, MONKEY, HUMAN and
RAT are very near. What is Pairwise alignment and
k-tuple ? Write the use of HSSP in Blast. [Marks 2 + 2 + 6 + 2 + 3]
============...
Course: B.sc
Subject :Computational Biology and Bioinformatics
Year of Question Paper : 2013
CS/B.Sc.(H)/MOLBIO/MICROBIO/BT/GENE/SEM-4/CBB-402/2012
2012
COMPUTATIONAL BIOLOGY &
BIOINFORMATICS
Time Allotted : 3 Hours Full Marks : 70
The figures in the margin indicate full marks.
Candidates are required to give their answers in their own words as
far as practicable.
GROUP – A
( Multiple Choice Type Questions )
1. Choose the correct alternatives for any ten of the following :
[Marks 10 × 1 = 10]
i) Each Gen Bank entry includes
a) a concise description of the sequence
b) the scientific name
c) taxonomy of the source organism
d) all of these.
ii) Methods to perform DNA or RNA sequencing include
a) chromosome walking
b) shotgun sequencing
c) chain termination method
d) all of these.
iii) Brookhaven .................. is a database of 3D
structures.
a) DDBJ b) PDB
c) Swiss Prot d) Uni Gene.
iv) Phylogenetic tree depends on
a) MSA b) BLAST c) Global alignment d) none of these.
v) Which of the following is not true about Swiss Prot ?
a) Highly curated
b) Highly cross-referenced
c) Non-redundant database
d) redundancy.
vi) The low complexity region among the following is
a) 'aaggtcctagtagtcga' b) 'aaaaaaaaa'
c) 'atttattaaagcgctgcat' d) 'nnnnnnna'.
vii) Dynamic programing is used to
a) develop the phylogenetic tree
b) detect the most suitable alignment
c) detect the conserved domain of different protein
d) none of these.
viii) Pairwise Sequence alignment is associated with
a) the Baum-Welch Algorithm
b) the Viterbi Algorithm
c) Needleman-Wunuch Algorithm
d) None of these.
ix) Blastx is a tool of
a) search protein database using a translated
nucleotide query
b) search nucleotide database using a translated
nucleotide query
c) search protein database using a protein query
d) search translated nucleotide database using a
protein query.
x) The E-value of an alignment
a) is the expected number of sequences that give the
same Z-score or better if the database is probed
with a random sequence
b) is expertise value of sequences that give the same
P-value
c) is probability value of an alignment having more
than these smilarities
d) none of these.
xi) Fasta algorithm uses
a) k-tuple values b) LSP values
c) complex values d) none of these.
xii) Gap penalty in sequence alignment is
a) the penalty score for umatch between later
b) the penalty score for umatch between two gaps
c) The penalty score for umatch between same
residues
d) the penalty score for giving a gap to get maximum
match interpreting as insertion. deletion and
mutation.
GROUP – B
( Short Answer Type Questions )
Answer any three of the following. [Marks 3 × 5 = 15]
2. What is Ramachandran plot ? Explain the utility of
Ramachandran plot to predict secondary structure.
3. How would you get the conserved domain and get the
phylogenetic relation of the prion protein of horse, human,
macaca mulatta and chimpanzee. What is Pubmed ? What is
the name of the database where you get the inheritable
disease of human ?
4. Explain the term 'GIR'. What is central dogma in biology ?
Give example of experimental and theoretical approaches for
proteomics.
5. Write short note on any one of the following :
a) MSA
b) The experimental approaches to genome sequence data.
6. What is substitution matrix ? In PAM-250 the 250 stands for
what ? Write down the difference of PAM250 and BIOSSM62
matrix.
GROUP – C
( Long Answer Type Questions )
Answer any three of the following. [Marks 3 × 15 = 45]
7. What are E-value and Z-value of an alignment ? Write down
the steps. Find a nucleotide from NCBI namely
Topoisomerase. Convert it to protein. Find the homologue of
the protein from the databases. Then find the similarity of
the corresponding protein with other species. What is pairwise
alignment and k-tuple ? Write the use of HSSP in Blast.
[Marks 2 + 2 + 6 + 2 + 3]
8. Explain the main features of CSD. Write the main features of
SCOP and CATH. Explain the information obtained from
PROPSEARCH method. [Marks 5 + 3 + 3 + 4]
9. Align the following two sequences by dynamic programming
method : 15
G A A T T C A G T T A ( sequence # 1 )
G G A T C G A ( sequence # 2 ).
10. Write down the name of the tools of NCBI where local
alignment is done. What is the algorithm behind the
program ? What are the applications of doing an MSA ? You
have beeen given a protein along with the sequence of it.
How would you identify the protein ? If not possible, then
how would you get an idea of the functionality of the
protein ? Give proper explanation. Define domain of a
protein. Write a short note on Blast's working procedure.
[Marks 1 + 1 + 2 + 3 + 1 + 2 + 2 + 1 + 2]
11. State the differences between homology and similarity.
Write down six emerging fields in bioinformatics. You have
given a sequence of African elephant and Indian elephant.
How would you draw the phylogenetic relation beween
them ? What result would you expect ? What is relative
mutability ? [Marks 3 + 3 + 4 + 2 + 3]
12. What is E-value and Z-value of an alignment ? Write down
the steps only. How will you show through bioinformatics
that the insulin sequence of HORSE, MONKEY, HUMAN and
RAT are very near. What is Pairwise alignment and
k-tuple ? Write the use of HSSP in Blast. [Marks 2 + 2 + 6 + 2 + 3]
============...
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