-C8MA1lCS

Lecfure Firsf
naeem ud Ahmad khaLLak
epaLmeL Cf Zoology
lslama College eshawa
(ChaLeed uesLy)
|0|NF0RHAT|68
computerited 4no/ysis
of 8io/oqico/ uoto
Cb[ect|ves
Introduct|on
ke|ated f|e|ds
n|story
AI1Lk 1nL kLSLN1 CCUkSL
W Lhe nuge data accumulaLed
W Us|ng the WWW
%%%%access Lhe daLa ad Lhe meLhods fo
Lhe aalyss
W App||cat|ons of 8I Lo
%%%%%molecula bology medce
boLechology agculLue foesc scece
aLhopology eLc
W
W the ro|e of computer sc|ence Lhe
%%%Aalyss of Lhe daLa
%%% fomaLo eLeal
%%%% ad Lhe ablLy Lo exLed Lhese
sklls by se/fdirected fie/d work on
the Web
W A sense of opt|m|sm
%%%% numan We|fare
AI1Lk 1nL kLSLN1 CCUkSL
1he Course Contents for 8|o|nformat|cs
W A lsghL Lo 8ofomaLcs
W 8ologcal aLabases
W 8ofomaLcs fo Cee(s) awse algmeL
W AlgmeL of MulLple Sequeces
W Seachg sequece daLabases usg 8LAS1 lAS1A
W hylogeeLc Aalyss
W Pdde Mako models
W Cee edcLo Mco aays
W 8ofomaLcs fo oLe(s) SLucLue edcLo
W yamc pogammg appleL
W 8asmol hylogey MulLple algmeL
WnA1 IS 8ICINICkMA1ICS?
W 8ioinformotics is the unified discip/ine o
combinotion of bio/oqy computer
science ond informotion techno/oqy
W 1he computer bosed ono/ysis of
bio/oqico/ doto
A MCLLCULAk ALnA8L1
W MosL b|o|og|ca| macromo|ecu|e
are po|ymers chas of mooomets
W All monomers be|ong to the same
genera| c|ass
W the order|ng of monomers ecodes
fomaLo lke Lhe leLLes of a
alphabeL
l1
lS
Slide 8
l1 THE SANE CENERAL CLASS, L!KE
NUCL!EC AC!DS: ATCC U
AND
AN!NOAC!DS: Leu, His, Ala ....... 20
lotus, 3/23/2011
lS SO !T !S TH!S !NFORNAT!ON CODED !N NUCLE!C AC!DS AND PROTE!NS THAT THE B!O!NFORNAT!CS HELPS US ANALYSE
BUT BEFORE CO!NC TO FURTHER DETA!L LETS CETS NORE FAN!L!AR W!TH B! BY D!SSCUSS!NC !TS RELAATED F!ELDS
lotus, 3/17/2011
kLLA1LD IILLDS
CCMU1A1ICNAL 8ICLCG
W applcaLo of compuLg meLhods fo
classcal bology
W maly coceed wLh
eoluLoay populaLo ad
LheoeLcal bology aLhe Lha Lhe
cellula o molecula leel
kLLA1LD IILLDS
MLDICAL INICkMA1ICS
W applcaLo of compuLg meLhods Lo
mpoe commucaLo
udesLadg ad maagemeL of
medcal daLa
kLLA1LD IILLDS
CnLMINICkMA1ICS
W 1he sLudy ad applcaLo of compuLg
meLhods alog wLh chemcal ad bologcal
Lechology for drug des|gn and deve|opment
kLLA1LD IILLDS
GLNCMICS
W Aalyss ad compaso of Lhe
ent|re qenome of a sgle speces o
of mulLple speces
W A qeoome set of oll qeoes possesseJ
by oo otqoolsm
kLLA1LD IILLDS
kC1LCMICS
W toJy of bow tbe qeoome ls
expressed in proteins ooJ of bow
tbese ptotelos fooctloo ooJ lotetoct
W oocetoeJ wltb tbe octuo/ stotes of
specific ce//s totbet tboo tbe
poteotlol stotes JesctlbeJ by tbe
qeoome
l2
Slide 14
l2 ie. CENONE !N ACT!ON, DYNAN!C STATE OF CELL
lotus, 3/23/2011
kLLA1LD IILLDS
nAkMACCGLNL1ICS
W 1he use of geomc meLhods Lo
deLeme whaL causes var|at|ons |n
|nd|v|dua| response to drug
treatments
W 1he goal s Lo deLfy dugs LhaL may
oly be effecLe fo subseLs of
paLeLs o Lo ta||or drugs for spec|f|c
|nd|v|dua|s or groups
nIS1Ck CI
8ICINICkMA1ICS
W CeeLcs
W CompuLes ad CompuLe
Scece
W 8ofomaLcs
l3
Slide 16
l3 $U!CKLY PASS!NC THROUCH THESE H!STOR!ES
lotus, 3/23/2011
nIS1Ck CI GLNL1ICS
W Cego Medel
W Chomosomes
W nA
Gregor Mende| (18221884)
W Lheoes of PeedLy
W Lhough Lhe sLudy of pea pods
W SLuded Lhem
fo Lhe fu of Lhe Lhg"
l4
l6
Slide 18
l4 YOU CAN RECALL THE CLASS!CAL NENDEL!AN CROSSES
ROUND X WR!NKLED
ROUND
3 ROUND 1 WR!NKELD
lotus, 3/23/2011
l6 SEE !F EvERY BODY UNDEERSTANDs NENDEL's CROSSES
lotus, 3/21/2011
Mende|'s Lxper|ments
W Cossbed Lwo dffeeL Lypes of pea seads
Specal
Wkled
W AfLe Lhe 2
d
geeaLo of pea seeds wee
cossbed Medel oLced LhaL alLhough all
of Lhe 2
d
geeaLo seeds wee sphecal
abouL 1/4
Lh
of Lhe 3
d
geeaLo seeds wee
wkled
Mende|'s Lxper|ments (cont)
W Medel deeloped Lhe cocepL of
#d|screte un|ts of |nher|tance" ad
W LhaL each ddual pea plaL had
two vetsloos ot olleles of a LaL
deLemg gee
Wa|ther I|emm|ng (18431903)
W SLuded Lhe cells of salamades
W mpoed fxg ad sLag
meLhods
W eeloped Lhe concept of mitosis
(1882)
n|story of Chromosomes
August We|smann (18341914)
W Soma ce||s and germ ce||s
W Lheoy of Lhe coLuLy of gem
plasm
W Lhe concept of meiosis
W S Sutton (18771916)
W sLuded gem cells of Lhe
tocbystolo moqoo (gasshoppe)
W uiscovered thot chromosomes
corried the ce//s units of
inheritonce
1 n Morgan (18661943)
W SLuded Lhe tosopblloe Lo deLeme
wheLhe heedLy deLemed
awsL eoluLo
W loud LhaL qenes cou/d be mopped
ode alog Lhe legLh of a
chomosome
n|story of DNA
W CffLh
W Aey MacLeod ad McCaLy
W Peshey ad Chase
W WaLso ad Cck
I Gr|ff|th
W l 1928 Lhe effecLs of bacLea o
mce
eLemed LhaL some kd of
transform|ng factor" exsLed
Lhe heedLy of cells
Avery MacLeod (187719SS)
W 1hough Lhe wok bacLea showed
LhaL DNA was the transform|ng factor
W DNA Lasfeg geeLc fomaLo
eously LhoughL Lo be a poLe
A|fred nershey (19081997)
Martha Chase (1930 )
W 1932 SLuded Lhe bacLeophage 12
ad Ls hosL bacLeum scbetlcblo
coll
W loud LhaL nA acLually
s Lhe geeLc maLeal
LhaL s Lasfeed
ames Watson (1928)
Iranc|s Cr|ck (1916)
W 1931 CollaboaLed Lo gaLhe all aalable
daLa abouL nA ode Lo deLeme Ls
sLucLue
W 1933 eeloped
1he double helx model fo nA sLucLue
1he A1CC sLads LhaL Lhe helx s cossLed of
@be sttoctote wos too ptetty oot to be
ttoe
!AMLS WA1SCn
W ogamable Mechacal CompuLe
n|story of Computers
Computer 1|me||ne
W 10008C 1he abacus
W 1623 Wlhelm Schckads mechan|ca| ca|cu|ator
W 1926 lsL paLeL fo a semcoducLo trans|stor
W 1939 Atanasoff8erry Computer created at Iowa
State
the wor|ds f|rst e|ectron|c d|g|ta| computer
W 1939 Lhe l8M ASCC)
W 1943 Collossus 8Lsh vacuum tube computer
W 1944 Cace Poppe ogamme
W 1943 lsL Computer 8ug
l7
Slide 37
l7 An analogy can be conceived between the monomerspolymers and small simplle wires and complex physical strucutres(used in the
makeing of transisters etc RECARD!NC THE STORACE AND/OR PROCESS!NC OF !NFORNAT
lotus, 10/1/2011
W 1948 Lo 1931 1he fsL commecal compuLe
W 1932 CWA umme cocees LegaLed ccuLs
W 1934 lC818An laguage deeloped
W 1963 Mouse eLed by ouglas LglebaL
W 1969 UNIk CS deeloped by keeLh 1hompso
W 1970 lsL sLaLc ad dyamc 8AMs
W 1971 lsL mcopocesso Lhe 4004
W 197S M|crosoft founded by 8||| Gates and au| A||en
W 1976 Apple mcocompuLes eleased
W 1981 lsL l8M C wLh CS
W 198S M|crosoft W|ndows
W 1992 ent|um processor
Genom|cs
W Ceome
compleLe seL of geeLc sLucLos fo makg a
ogasm
W Ceomcs
Lo aalyze CLnCML
Wa|ter G||bert and Ireder|ck Sanger won the
Nobe| r|ze |n 1980 for the |nvent|on of DNA
sequenc|ng |n 1977
Laly geomcs was mosLly ecodg geome
sequeces
PsLoy of Ceomcs
W 1980
lsL compleLe geome sequece fo
adeous s publshed
W lx174 3386 base pas codg 9 poLes
W 3kb
W 1993
oemopbllos lofloeozeo geome sequeced (flu bacLea 18
Mb)
W 1996
occbotomyces cetevlsloe (bakes yeasL 121 Mbp)
W 1997
coll (47 Mbp)
W 2000
9seoJomooos oetoqlooso (63 Mbp)
melaogasLe geome (180Mb)
2001 1he 8g Ce
W 1he Puma Ceome sequece s publshed
3 Cb
WhaL exL?
W osL Ceomc ea
CompaaLe Ceomcs
lucLoal Ceomcs ad SLucLual Ceomcs
oLeomcs
roteom|cs
W Lhe sLudy of Lhe poLeomeLhe
#kC1L|n comp|ement of the
genCML"
W Lhe qualLaLe ad quaLLaLe
compaso of poLeomes ude
dffeeL codLos Lo fuLhe uael
bologcal pocesses
What Makes roteom|cs Important?
W A cell's DNA|ts geomea b|uepr|nt fo
Lhe ce||'s potent|a| all Lhe possble foms
LhaL L could coceably Lake
W lL does not descr|be the ce||'s actua|
current form
What Makes roteom|cs Important?
W All cells a ogasm coLa Lhe same nA
W 1hs nA ecodes eey possble cell Lype
LhaL ogasmmuscle boe ee sk eLc
W lf we waL Lo kow abouL Lhe Lype ad sLaLe
of a paLcula cell Lhe DNA does not he|p us
W Lhe same way LhaL kowg whaL laguage
a compuLe pogam was wLLe Lells us
oLhg abouL whaL Lhe pogam does
W Iew a webpage ad Ls souce by 8ghL
ClcknL1 acLceP88hLm
What Makes roteom|cs Important?
Cut of the thousands of genes on|y a handfu|
actua||y determ|ne that ce||'s structure
Many of the |nterest|ng th|ngs about a g|ven
ce||'s current state can be deduced from the
type and structure of the prote|ns |t expresses
Changes |n for examp|e t|ssue types carbon
sources temperature and stage |n ||fe of the
ce|| can be observed |n |ts prote|ns
roteom|cs In D|sease 1reatment
W A lage umbe of dseases ae caused by a
paLcula paLLe a goup of gees LC?
W lsolaLg Lhs goup by compag Lhe hudeds
of Lhousads of gees each of may
geomes would be ey mpacLcal
W Look|ng at the proteomes of the ce||s
assoc|ated w|th the d|sease |s much more
eff|c|ent
roteom|cs In D|sease 1reatment
W May huma dseases ae
caused by a omal poLe
beg modfed mpopely
W 1he LageLs of almosL all
medcal dugs ae poLes
Lxamp|es
W WhaL do Lhese hae commo?
Alzhemes dsease
CysLc fboss
Mad Cow dsease
Stan|ey rus|ner
prion protein
s a norma| poLe fequeL lg ogasms
Whe some po chage Ls shape by mssfoldg L
becomes r|on%%% a fecLous ageL
W un||ke other kow fecLous ageLs whch musL
coLa uclec acds alog wLh poLe
compoeLs
W r|ons come dffeeL sLas each wLh
a slghLly dffeeL sLucLue ad mosL
sLas beed Lue
W o eplcaLo s eeLheless sub[ecL Lo
occasoal epmuLaLo ad Lhe aLual
selecLo [usL lke oLhe foms of
eplcaLo
W Lhe umbe of possble dsLcL po
sLas s lkely fa smalle Lha Lhe umbe
of possble nA sequeces so evo|ut|on
takes p|ace w|th|n a ||m|ted space