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D~artment

April 29, 2008

of Biochemical Engineering & Biotechnology
BE 418: Bioinformatics
Major Test

Time: 2 hour M.M: ~

v/Describe the shotgun cloning method of gene sequencing. How it is coupled to modern day high
throughput sequencing? What are the two serious bioinformatics implications of this method? @

~ Diagrammatically show the protein structure hierarchy. What different public domain databases are

available for protein information? Jib t-~ f\- ~ oJo..G c7J1l l fJ~ s7 ( Q)
~ExPlain various indicators that help to give the level of confidence while evaluating a relationship
between a query sequence and other sequences existing in any database. ~

A'fiO' 'h, "'m 'Patt,rn match;og'.How import.nt;, till' con"pt in Bioiofmmati,,? ~

A nucleotide sequence can normally be divided into five different categories of sequences based on its
~ "'It..
~:~tional constraints. Comment on the relative substitution rates in each category along with the reasoning
given for each state e.g. broadly coding sequences substitution rate is less than that of non-coding
sequences substitution rate. Q)

~ an~
Write briefly on the concepts, namel~ Mutation vs Substitutions (0.5) ~kes-Cantor
Molecular Clocks & Relative rate tests m.
Model M)
@
JA. Dmw the phylogenetic tree (use std symbols) that corresponds to the one described in the standard
Newick Format as «(A, B), C), (D, E), F). Number the internal nodes using Roman numerals I, II, iiI, ...
How many internal nodes are created? (1+0.5+~ m
~raw all the possible unrooted trees for the species A, B, C, & D and only 8 out of all the possible
rooted trees of these four species. (1+6) (J)

~se UPGMA to reconstruct a phylogenetic tree using the following distance matrix. Using this example
expl '-'-.
Species A B C D
B 6 - - -
I ~~~
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C
D
12
18
10
18
-
20
-
-
E 24 22 26 18

~ Briefly describe Parsimony Method of phylogeny with the help of an example. The concept of
informativesiteanduninformativesite shouldalsobe explained. (2.5) ...

J. W"" ,hort oot" o~"oo" ,xon, andal;,;o." 'PI;Ci~'ochore' ane/J g,oe d,n,ity. (4.5)

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