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D~partment of Biochemical'~l1gin!ering and Biotechnology

\' BE488:,iJi6ll1rorinatics
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MAJOR TEST~H (Date: 8.~~200~,Time: :3~17:3~ hOursl"~Yenue: 111374)'11

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Answer allquestiorl-s Time: 2 hour
"" " ,.,' . M. Marks: 35

How do you relate .yourte~paper--J~eicJ'!() the. broad fipld of bioinformatics?.

What led you towriteyo~r term, paper7:'W¥f is the srope ahd futUreof your tenn
paper area in the field cit bioirtf°milit!cs?'fie brief" scientific and logical. The
answers using schematicsltableslbulletsystetrtwin he prefelTed~, (5 marks)
What are,the aims of pr?teomics research?~~\¥ll~t
are the generalmethodology you
wouldadopt in proteomeanalysis,deS'cribe
schematically?Whatare ,thc\Vaysone
caI1<;,hec~
purity otapr6tein?" '.>:~~<, i.~;'j'~ ;It; 'it (4m8fks),';k
t'i Givt{~ou,rVic\vg'to ,t~~~oll~f~~~'§'~~g di~CoyerY~~heri!~you' are
, 199Jg,pg'f9ft,a;, ta}-g~t dflig~fu91~~ \if is.' '~tg,:'~~7JrW)~~J '

'"'pr~ou;}[6"Ufcf statlil'~""b~{t~3rt1'~i>'~ffi~' J",' '. f.~.iW", .

. .

C! 4+2 marks)
Seg~,~!,1(S~"".. .",... ' '.." "'--'" ., ".-.---
. ,,- . ""-'--""-"' j
]N'<line i ~qjuence "' '--"'---"---'--'-'---"'--"'.-'" , '

~::~~:~~"..~-i~
I
Sequence C ACGCAATGAA
.~.~uenc~12__~1.ACACAGGGAA =~~
Draw a distance matrix where distance is defined as edit distance (the number of
mutations required to transform one sequence to the another). Test ifthis distance
matrix shmvs uitr3m~tric ;\ddi1ivetree- If not give the n~asons, .
l. SCClUedces

! N;'.~e ."-[~~qt;~; ~;'~'-"-~~==~~':-~==~"~~~~~',=:~-~~~,".:_.=~:,

"-~~:"~-'~",~..=.::'=]
I ~equence
" ," , n.-
i ACGCGTTGGGCGATGGCAACi
.L. ..., _.'.."., ,.,.,.,, '-'--"' ' " ,-..,-,-.---

j Sequence B -, ! ACGCGTTGGGCGACGGTAAT I ... . '. .

~:§,~sili.;i~~~~==-~,-~~ri~CGCXf~~E~L_~tqEtQl~t~1t=.:"..=-.,=='=.'." '. ., - "._."::--='.=.~=~~..!

: SCGucnccD
L 1.:
I ACACATTGAGTGATAAL\A
' ,.-,
T ,.-.,., '~._.'-"-'--".'--"-' ' ,
i
,-~~,.--'" J

Find the distance matri>( and phylogenetictree u$ing Fitch MargoHash algorilhm,
 .

(4+4 marks)

51\. Oq\lill~ ,of' l.l~M? I\,\~I (\~8tl'\bQ ~H~p.hy"~l~~p

tbe \hr~Qdilrcrqn(,."m)pllCt)~iohS
methodf()t'id~l\lityin8Jh~~tj1il~()fa
," "...",'. particularPJolcin sequence.
f
lb.1<.StH:Fmd thebpiiijilJln.siate;'seq~~tic~~singViterb~
mgorithm for the observation I
sequence offour-lengths, ifthe'w~ights for transition between the'states are,given
as follows ( figure 1, where the circled numbers are the initiai weights of the
corresponding states). (2+4 marks) . <

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Department of Biochemical Engineering & Biotechnolog)' ~
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BE 488: Bioinfo,rmatics
Major J:,es!L 2 ' ,~'

May 9, 2005
, ' I' ~b;~, .' Time: 2 hour'
" .M.M: 40

Kindly answer PART-A & PART-B on separate answer sheets. To facilitate f

'4yaluation, please try to answer in the serial order. ,

PART-A
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"la. Importance of sequence alignment in Biojnfotmatics and briefly describe methods used, .f
!
in ,sequencealignmenHo reflect evolutionarY'clulOgd: 'r, , /~@

'b. , 'Role ()f'Substitutiott Matrices'iri sequenc~,~Hgn.p~nt." ""M> ~.l I

c-~ ~~"'~Ela9~rateareas~i~'Do 'Ibis are apli -h', .,";;; '",'h<'" ,> ~,>\,:, ~ -"
~
):;, I
~;J
,i,'" ;~'Et,.,. J"': 'f<»" ;;ir,..~', ~~: , ~,t~,f"~~' ,', ,~~,!
2. ">'.\vh~tdo~~uun., t, ""C"",." " ,~.' ., ,', , "",~~!Q!~lhg?~'~C~~;#1~:J~~.g",~a.~'~'"
J; , hydrophobic zippef!ltS~ssit5te ffi~chah , , ;;~< tidijibf
secokaar}1'fiSt"rU ""'" , "

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,:' ,~."", ,"",,"" . ",', " . ' '" "" ,'jif'" ,,', r'-j.,~"',w""'" ~
,'Ijj ""!'
proteins' :1,~i!i"1fi~¥ ~{tf.o, "" ~~ '" " ~'t~ "ri'~ 1;""'<.\,,$W"t~~ ,~:), ,
" '~', <J'%,r " ,"" S ,j,t"~,,>,;,, 't'c ,: ~;<;f:' ~"":"'"~::~2 ,i; ~;,\, "i;;;~,~li~t;. "'1

Describebriefly'the getlestructure of a'typI~I"~lIkar9QiicptgarijsmJ!ighlightirig (i} "t"~;"

I Promoter elements & Regulatory protein biridiilg'§ites Vi) Transcription Factors 8iroleof ~,
, hnRNAs (iii) I;ltrons, exons and altl:rnate splicing. BrjeOy comments on the presence of
, " similar/dissim:lar features in prokal)'otes;:, , {(J. x 3) 2 + 1.5=W.5}
'>',,' "" .{;;,,~t,: :,,' "
I '
Write short nofe on eacl1of the foll{jwing:~" """ (

(i) CpG Islands(ii) fsochores(Hi)Repetitiveelements& eukat)'oticgenedensity"" ! j

" (1.5x3=4.5)

PART-B

Sa, , A person is playing with the two one rupees coins. Both arc biased to produce head (1;)
\"ith the probability 0.8 and 0.9 respectiv,el:/;He tossesthe first c()in twice and second
once and then repeats this sequence again. He produces HHHTHITHH, Find the
I
I probability of producll1g this observation sequence? ' m
, b. Which one is more probable to be a translation start?
CACC ATG GC or TCGA ATG IT. Using following table find the support for your
ans\ver.
r, I
,', ' I ATG I --

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(j 1,
(j ,~ 3 - >' - ..:.
~
8,,'J
r,
' 3 51,,
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8"
5
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"'~"'"'I''~;"' :'' ", ",9" ' 3,,9 " ,)7 ' ' '0:":,4 .l.' '" '
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6a. Explain molecular clock theoryI, II and m. and their uses in distance measurements
ultramctric, UPGidA, maXilIiul11parsimony 3nd maximum likelihood methods. O, ".,

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 b. Anevolutionarytree is to be'buildup in orderto 1111d~fStandthe lineage between the class
of birds based on the five differ~nt~aits 1:white'C9,lpur,2: averagelength(=1Ocmsad I

above), 3: thicl5.ness(=1 ems ancf'hbove),4:'average-'numberof feathers (=10 and above),

and 5: sharpness at the free eod pfthe feathers (=exhibiting angle at end as 30 degree or
below). FiVetypes of the birds show these sets of observable features such that qird A
exhibits J and 2 characteristics; bird B exhibits 3 characteristic, bird C exhibits 1,2 and 5
characteristics, bird D exhibits 3 and 4 characteristics, and bird E exhibits 2 characteristic
only, Sho\\' the phylogenetic tree. Q.)

7a. In which ways are 'sequence profile' methods better than 'searching for motifs' method
in classification of proteins? a) I

b. SCQPis a hierarchical databaseof protein structures{i}\Yhat is the difference between i'

members of a 1~lInilyand aS4perfamily? SUPP9r.!..YPuf.0"answer "Yithan example, (ii) I
of protein families~wb\qhexhibit a;'seque!\~~;si1pilarirY
less than 20% mgy stiII, I
I1JJ*Sl~Hx~~q~~~f~~~~~~tn.:l~~~:i1~~'i~1~~t~",~;;~~~~.,~~S-~~

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B. "\'AM250" matriX is n\Die used in comrt10nfot'stqucnec aligrtri,2nl.'Whit

,arious
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pAM..,'"
.Mwice> availahle for
.
usl; ",rd w'ml. .'
into)1na\!bnis
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conveved
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I"' the number
in (\lis.matrix'ns"""?' ..
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3A. A nucleotidc sequence can ow"'"",' e; Glvided inlO fivc' di\lercru c'dlegorie~"C
\ sequences based on its functional Clm,trainIS,(:ommcnt on therelslive subStitulionralcs
Q)
\ in cuch along with I"e reasoning givtt1 for coeh state c,g. h[()adly coding
s"O,HenerssubslitutiOl\rate is Ie,', than that 0r non codin!.. """,e
> :;cOS
subs!imtion"" te.

(~)
B. Writebrieflyon the fo!low1.ngconcep1 ill2.)
(i) MutationvS Substitutions C
(8)
(ii) Fi~ations (8)
(iti) Jukes-Cantor 1'v1ode\ (~)
(!\,) Kinwra l\'1odc\
i (\) \\okcu\m CioCKs&. Relative ratc \'.;S15
I
I
H. \J ren' lhe ph Y'(1~e ndic tree \ r>sesed ,yn\b"ls) thot cones\," nrb to \\1epno ,lcse tii,cd i"
the standard Newick \'oir""t as (((1\, B). C), (D,E), F). NUh,bcr the inlcrnal nndes usiug
Roman nU\11eral$I. \1. \1\. ... !low ",any i"lcrrr~\ ""dcs '1fCcrea"d')ll+~+~)

, n. Draw all the pqsSiblc unrootcd Irees for me ,pc"'ie. A, B, C, & D. Draw only S out of
ail the possible rooled trees qfthese fqut species, (1+D

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SA. UseU POM ;$1&) feco":tf\(e::J~~r.lii'(;e~!ollsi

ng the foilowing distance "wirix:
Y,., . .. . '..Y'\tiJij,i;~i,~,:;;~'>C.~ .."

rsp.~i.r°(r'-'~'--~::i:" c' B-~~1-C ,,~c'i-- 1

[=~-t~~:!~~¥~~~t~:_~~~=L~--~.~:j (I)

U. Briefly describe why the first fOUfpositions of the following table arc uninformative
andthe lasttwOpOsiti(i!1sarcinfqrn1~liy~
, rriP~rsil11onyMcthod
. of phylogeny:

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