DEPARTMENT OF CHEMICAL ENGINEERING

IIT BOMBAY
CL 662: INTRODUCTION TO COMPUTATIONAL BIOLOGY
HOMEWORK 4 Due on 23/02/2018.
Note:

1. You are expected to answer the assignments in your own words. Cite references and websites /
web servers wherever possible. Copying from any source or from other students in the class (or past
students) will result in FR grade. Both the source and sink will receive the same penalty in cases of
copying. Therefore, please do not share your work with others even after the deadline.

2. Note that you will need to refer to text books, research or review articles, web sources, databases
or web servers to answer some of the questions. You are expected to find an appropriate source
when not mentioned in the assignment. Please cite your source.

3. Report concise summary of your results and analysis rather than submitting pages after pages of
output from a software program. Your comments on the results will carry weightage.

1. Choose 2 proteins predicted in assignment 2 of your choice. Carry out a BLAST operation to
find a matching protein sequence for each. Now align these two sequences locally as well as
globally using an online tool (e.g. http://www.ebi.ac.uk/Tools/psa/) for both proteins. From
the local and the global alignment choose an alignment of length 7 amino acids (it should
have some gaps). Align it manually using dynamic programming (Smith-Waterman algorithm
for local alignment and Needleman-Wunsch algorithm for global alignment). Use the same
parameters (gap opening penalty, gap extension penalty and substitution matrix) that were
used in the online tool. Clearly bring out the differences in the local and global alignment in
your manual alignment.
[9 marks]

2. Write a short note on how to predict the pI (isoelectric point) for a given sequence of amino
acids. Explain briefly the rationale used by online tools that predict pI.
[3 marks]

3. Explain Gapped BLAST and PSI-BLAST considering how they are different from normal
BLAST? How do these programs work? How is PSSM calculated in PSI-BLAST? What are the
different parameters considered in the calculation and their significance? Explain the
calculation procedures with example. You may refer to the article on this topic by Altschul
et al. 1997. Also, show how PSSM looks for a representative example and analyse how it
differs from BLOSUM62 matrix by using specific examples.
[8 marks]

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