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Department of Biochemical Engineering and HiotechnoJog)'
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BE488: Bioinformatics (~lajor Exam)
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Dated: 6.5.04
J Time: 2 hours
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I Answer all the questions
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I (a) Draw the three alternati\ e unrooted trees for four taxa whose nuclcotides at a
position under consideration are T.T.C, and C. Label each of the internal nodes with
i the most likel~' candidates for inferred ancestral sequence~ Ho\\' man~' of the"
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'\ possible unrooted tree for the taxa used in this question. arc equa1lvparsimoniusin
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1 " that they invoke a minimum of one substitution') How many invoke a minimum of
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i t\\'o substitutions'1
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, (b) In :1 gi\"en pairwise similarity matrix, find the phylogenetic distance based tree
using UPG~\'1A'} State all the assumptionsmade in developingthis tree,
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A } (c) Answer the following:

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~. 1. How many nuc1eotid~long would a DNA sequence need to be in order
for it to not be found b)' chance more than once in a genome whose size
is 3 billion base pairs long?
.,. II. Assuming that all amino acids are utilized with the same frequency and
that there are " total of approximately1000 umquedestinationsfor a
,
~. protein\vithina eucaryoticcell,whatis the minimumlengththat a signal
sequence must be to ensure that its associated protein w1ll be delivered
appropriately?
(5+5+3 (=1.5+1.5) marks)
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2 (a) Consider on H!\.1Mwith a sequence ofM match states each of which can generate
J. a letter 'x' ITom the alphabet of amino acids corresponding to a distribution
\ P(x/mk), k = 1..,... ,\1. For each match state mk consider a delete state dk and
t insert state h LTsea dumrr.ybegin state and a dumm) end state. denoted by mo
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and m~I-'1respectively. draw the architecture of such on I-L\1Mmodel and label all
.1 transitions probabilitiesin the diagram,Assume that transitionsinto match or
delete states alw-ays.move forward in your model, but that transition into insert
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states do not move forward- .

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(b) The differencesbetween loca! and global sequence algor.thms have already been
1!1i discussed i1ldetails. \\"hat are s;milaritiesbetween them?
(10+3 marks)

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3 (a) Brie11yexplain rl1\;tf)!!owing terms' - (i) Mutations or subsriIUtion rates: (ji) lnde1s
and p~l;'ltduge!lI;~. (iil) Synonymous and !\~\J/Jsynony:nUllS ~llbsliwtions; and
Ov) Traw;ition \5 Transversions (O.5X4==2marks)
(b) Briefly discuss the Juke's Canter mode! for es!irnaringthe actual substitution rates
."",.. between two sequencesfromthe obs$3rved substirurioffrates. (3 '.narks)
4. Write a brief note 01' ~he following. - (i) Promoterelementsof ProKaryotes,(ij)
Promoter elements \.,fEucaryotes; (iii) GC contents in Prokaryotes and Eucarymes; 7th
(iv) Isochores (2X4==8marks) 1.0i
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