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Transcript of bioinformatics semester 8th
-
8/10/2019 bioinformatics semester 8th
1/14
Yashwantrao
Chava
n
Maharashtra
Open
Univers
ity
M.Sc.
inBio-Informatics
SyllabuS
Yashwantrao ChavanMaharashtra
Open UniversityDnyangangotri, Near Gangapur Dam,
Nashik 422 222, IndiaPhone: 0253-223!4, 223!5, 2234!3
"a#: 2234!3$ 223!%&mai': s(te(h)y(mou*(om
+esite: http:$$*y(mou*(om$
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Bio-Informatics Proramme Curriculum Pae 1of 14
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Contents .harts and /a'es *************************************************************************************************************3
* io-In1o rmati(s Programme tru(ture .harts **************************************************************3
*2 io-In1o rmati(s Programmes Detai' s ***************************************************************************4
*3 ioin1ormati(s .ourse Detai' s **************************************************************************************4
*4 .ourse Distriution .hart ********************************************************************************************52 y''aus ***************************************************************************************************************************%
2* emester 0 ****************************************************************************************************************%
200, .678* 9'' ights eser;ed*Price: Indian s 200$- or 8< 50$- on'y* "ree Don'oad o1 Internet =ersion*Last Update: aturday, >une 2!, 200?Printed By:Publisher: egistrar, .678, Nashik 422 222, India*
Bio-Informatics Proramme Curriculum Pae 2of 14
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! Charts an" #ables
!.! Bio-Informatics Proramme Structure Charts
!.!.! $or O"" %umbere" SemestersMandatoryCS Month
September October November ecember !anuary
OddNumberedSemester
Course 14 CP" #heory
Course
Course 24 CP" #heory
Course
Course $4 CP" #heory
Course
Course 44 CP" # heory
Course
Course %4 CP" Practical or
Pro&ect'(or) Course
0I0:
asi( io'ogy
I02:.ommuni(ation
ki''s
I03:6athemati(s
I04:&n;ironmenta'
(ien(e
I05:@a, .ourse
03
I03:asi(
io(hemistry
I032:Genera'
6i(ro,io'ogy-I
I033:Physio'ogy
I034:6eta,o'ism
I035:@a, .ourse
05I05:asi(s o1
ioin1ormati(s
I052:.omputer
Programming-I
I053:
D6-I
I054:Introdu(tion to
6o'e(u'arGeneti(s
I055:
@a .ourse
0!
00!:.on(epts in
.omputing andasi(s o1
ioin1ormati(s
I0!2:io'ogi(a'.hemistry
I0!3:tatisti(a'/e(hniAues
I0!4:tru(tura' io'ogy
I0!5:@a .ourse
0?I0?:
io(hemistry o16etao'ism
0?0?2:eAuen(e-asedioin1ormati(s
9pproa(hes
I0?3:Programming
@anguages ando1tarte /oo's
inioin1ormati(s-I
I0?4:Programming
@anguages ando1tarte /oo's inioin1ormati(s-II
I0?5:@a .ourse
!.!.& $or 'ven %umbere" Semesters
MandatoryCS Month
March *pril May !une !uly
+venNumberedSemester
Course 14 CP" #heory
Course
Course 24 CP" #heory
Course
Course $4 CP" #heory
Course
Course 44 CP" #heory
Course
Course %4 CP" Practical or
Pro&ect'(or) Course
02I02:
asi( tatisti(sI022:
asi( .hemistryI023:
9pp'ied Physi(s
I024:Programming
.on(epts
I025:@a, .ourse
04I04:
.e'' io'ogy-II042:
asi( ios(ien(es
I043:iophysi(a'
/e(hniAues-I
I044:6o'e(u'ar io'ogy-I
I045:@a, .ourse
0%
I0%:.omputationa'
6o'e(u'ario'ogy
I0%2:.omputer
Programming-II
I0%3:D6-II
I0%4:.e'' io'ogy,Geneti(s B
Immuno'ogy
I0%5@a .ourse
0
I0:Genomi(s
Dataases and9pp'i(ations
I02:Geneti(
In1ormation"'o and
Pro(essing
I03:Programming in
Per'
I04:Protein tru(ture
Predi(tion and6o'e(u'ar6ode'ing
I05@a (ourse
0I0:Geneti(
&ngineering
I02:Geneti(s and
Genomi(s
I03:Dataase
6anagementystems
I04:esear(h
6ethodo'ogy
I05ProCe(t
Bio-Informatics Proramme Curriculum Pae $of 14
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!.& Bio-Informatics Prorammes (etails
SN Pro,ramme -or certi.ication" student must con.irm tospeci.ied certi.ication eli,ibility criteria and.oll o/in, courses spec i.i ed .or therespective pro,ramme must be success.ullycompleted
Post'0raduate e,ree Pro,ramme
6*(* io-In1ormati(sE 9'' 20 (ourses at semester 0! to 0
0raduate e,ree Pro,ramme
*(* io-In1ormati(sE 9'' 30 (ourses at semester 0 to 0%
!.) Bioinformatics Course (etails
.P: .redit Points
./: .ounse'ing ession /ime/: e'1-tudy /ime.at: .ourse .ategory 1rom the e'o:
: asi( (ien(e em 0-02E
D: Dis(ip'ine asi( em 03-04E D.: Dis(ip'ine .ore em 05-0%E
.: pe(ia'iFation .ourses em 0!0E/ype: .ourse /ype 1rom the e'o: /: /heory
P: Pra(ti(a' P: eminar or ProCe(t-+ork
SN Semester Course
Code Name CP CS# SS# Mar)s Cat #ype
!
I0 asi( io'ogy 4 40 20 00 /
2 I02 .ommuni(ation ki'' 4 40 20 00 /
3 I03 6athemati(s 4 40 20 00 /
4 I04 &n;ironmenta' (ien(e 4 40 20 00 /
5 I05 @a .ourse 4 0 20 00 P
%
&
I02 asi( tatisti(s 4 40 20 00 /
! I022 asi( .hemistry 4 40 20 00 /
I023 9pp'ied Physi(s 4 40 20 00 /
? I024 Programming .on(epts 4 40 20 00 /
0 I025 @a .ourse 4 0 20 00 P
)
I03 asi( io(hemistry 4 40 20 00 D /
2 I032 Genera' 6i(roio'ogy-I 4 40 20 00 D /
3 I033 Physio'ogy 4 40 20 00 D /
4 I034 6etao'ism 4 40 20 00 D /
5 I035 @a .ourse 4 0 20 00 D P
%
*
I04 .e'' io'ogy-I 4 40 20 00 D /
! I042 asi( ios(ien(es 4 40 20 00 D /
I043 iophysi(a' /e(hniAues-I 4 40 20 00 D /
? I044 6o'e(u'ar io'ogy-I 4 40 20 00 D /20 I045 @a .ourse 4 0 20 00 D P
2
+
I05 asi(s o1 ioin1ormati(s 4 40 20 00 D. /
22 I052 .omputer Programming - I 4 40 20 00 D. /
23 I053 D6 - I 4 40 20 00 D. /
24 I054 Introdu(tion to 6o'e(u'ar Geneti(s 4 40 20 00 D. /
25 I055 @a .ourse 4 0 20 00 D. P
2% , I0% .omputationa' 6o'e(u'ar io'ogy 4 40 20 00 D. /2! I0%2 .omputer Programming - II 4 40 20 00 D. /
2 I0%3 D6 - II 4 40 20 00 D. /
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SN Semester Course
Code Name CP CS# SS# Mar)s Cat #ype
2? I0%4 .e'' io'ogy, Geneti(s BImmuno'ogy
4 40 20 00 D. /
30 I0%5 @a .ourse 4 0 20 00 D. P
2%
00! .on(epts in .omputing and asi(s
o1 ioin1ormati(s
4 40 20 00 . /
2! I0!2 io'ogi(a' .hemistry 4 40 20 00 . /
2 I0!3 tatisti(a' /e(hniAues 4 40 20 00 . /
2? I0!4 tru(tura' io'ogy 4 40 20 00 . /
30 I0!5 @a .ourse 4 0 20 00 . P
2%
I0 Genomi(s Dataases B 9pp'i(ations 4 40 20 00 . /
2! I02 Geneti( In1ormation "'o andPro(essing
4 40 20 00 . /
2 I03 Programming in Per' 4 40 20 00 . /
2? I04 Protein tru(ture Predi(tion B6o'e(u'ar 6ode''ing
4 40 20 00 . /
30 I05 @a .ourse 4 0 20 00 . P
2%
/
I0? io(hemistry o1 6etao'ism 4 40 20 00 . /
2! 0?0?2 eAuen(e-ased ioin1ormati(s9pproa(hes
4 40 20 00 . /
2 I0?3 Programming @anguages ando1tarte /oo's in ioin1ormati(s-I
4 40 20 00 . /
2? I0?4 Programming @anguages ando1tarte /oo's in ioin1ormati(s-II
4 40 20 00 . /
30 I0?5 @a .ourse 4 0 20 00 . P
2%
!0
I0 Geneti( &ngineering 4 40 20 00 . /
2! I02 Geneti(s and Genomi(s 4 40 20 00 . /
2 I03 Dataase 6nagement ystems 4 40 20 00 . /
2? I04 esear(h 6ethodo'ogy 4 40 20 00 . /
30 I05 ProCe(t 4 0 20 00 . P
!.* Course (istribution Chart
!.*.! 1s per Course Cateory
SN Course Cate,ory No o.Courses
CreditPoints
o. CreditPoints
Counselin,ours
o.Counselin,
ours
: asi( (ien(e 0 40 20H 40 20H
2 D: Dis(ip'ine asi( 0 40 20H 40 20H
3 D.: Dis(ip'ine .ore 0 40 20H 40 20H
4 .: pe(ia'iFation .ourses 20 0 40H ?%0 40H
% #otal %3 233 133 2433 133
!.*.& 1s per Course #ype
SN Course #ype No o.Courses
CreditPoints
o. CreditPoints
Counselin,ours
o.Counselin,
ours
/: /heoreti(a' 40 %0 0H %00 %!H
2 : ki'' ased P and P+E 0 40 20H 00 33H
$ #otal %3 233 133 2433 133
Bio-Informatics Proramme Curriculum Pae %of 14
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& Syllabus
&.! Semester 0
&.!.! SBI0!
Code Course Name Pro, Sem CP CS# SS# Mar)s #ype Cat
I0 Genomi(s Dataases B 9pp'i(ations I 4 40 20 00 / .
Course Prereuisites:
asi( kno'edge aout io'ogi(a'dataases
Course Ob&ectives: 91ter su((ess1u' (omp'etion o1 this(ourse, student shou'd e a'e to
8nderstand the ro'e o1 ioin1ormati(s in thegenome seAuen(ing, assem'y, annotation andpost genomi( ana'yses 1or gene identi1i(ation,s tru(tura ' and 1un(t iona ' e 'u(idation o 1genomes, drug target identi1i(ation et(*
5emar)s6
UN Name o. Unit CP CS# +valuation Pattern rosing Genomi( esour(es 0
9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
2 Data 6ining /oo's 2 0 9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
3 @inking Genotype to Phenotype 3 0 9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
4 9pp'i(ations o1 Genome Data 4 0 9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
UN etai l Sy llabus o. the Un it
Bro/sin, 0enomic 5esources6
Genome 9ssem'y o;er;ie
e'ated data resour(es &/, /, G, E et(*
Genomi( dataases at &I and N.I
Genomi( dataases 1or human, mouse, yeast and other mode' organisms
Genomi( dataases 1or p'ant, mi(roia', parasite and ;ira' genomes
.ha''enges in de;e'opment o1 genomi( dataases B resour(es
2 ata Minin, #ools6
asi( 9spe(ts o1 Genome 9nnotation
rosing genomi( data using &nsem' &IE and 6ap =ieer N.IE
Predi(tion o1 7"s and GenesJ Gene 6ode'ing,
Gene predi(tion a'gorithms 1or prokaryotes B eukaryotes
Predi(tion o1 igna' seAuen(es Promoters, Primers, sp'i(e sites, 8/s et(*E, 7perons
3 Lin)in, 0enotype to Phenotype6
uman B mouse genome: 76I6 dataase
Identi1i(ation o1 Disease Genes
@inking human genome data, 76I6 dataase and NP dataases
uerying genomi( data 1or ;arious diseases
Identi1i(ation o1 homo'ogous genes: 7rtho'ogs B Para'ogs
@inking genomi( data in the (onte#t o1 metao'i( pathays
4 *pplications o. 0enome ata6
Bio-Informatics Proramme Curriculum Pae 7of 14
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Genome ased drug design
Genome ased ;a((ine design
6i(roarray ana'ysis B too's
Proteomi(s ana'ysis B too's
tru(tura' genomi(s
"un(tiona' genomi(s
Boo) Code #it le"*uthor"8SBN o. Ori,inal +dition
etails o.Chapters and Sections8ncluded in Syllabus
+dition9ear
Publisher"Price"Order 8t ere
#e:t Boo)s
I0-/ Prin(ip'es o1 Genome9na'ysis 9nd Genomi(s 3rd&d*E y Primrose, ** B/yman, *6*
In('uded:
('uded:'a(ke' ' Pu'ish ing
.ompany, 2003*
I0-/2 /he Genome
am * =erma
IN -5%0-043-2*
=.
5e.erence Boo)s
I0- Genome mapping andseAuen(ing y IanDunham,
oriFon, IN-
?4%-50-%*
Bio-Informatics Proramme Curriculum Pae ;of 14
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&.!.& SBI0&
Code Course Name Pro, Sem CP CS# SS# Mar)s #ype Cat
I02 Geneti ( In1ormation "'o andPro(essing
I 4 40 20 00 / .
Course Prereuisites: Kno'edge o1 geneti( materia' in
prokaryotes and eukaryotes
Course Ob&ectives: 91ter su((ess1u' (omp'etion o1 this(ourse, student shou'd e a'e to
8nderstand (on(epts in gene organiFation,trans(ription, trans'ation and gene regu'ation
9ppre(iate iote(hno'ogi(a' imp'i(ations o1re(ent de;e'opments in ('oning and genomeseAuen(ing
5emar)s6
UN Name o. Unit CP CS# +valuation Pattern
Gene pression 0
9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
2 Genes and &nFymes2 0
9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
3 Genes N9 and Proteins3 0
9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
4 Gene pression and 6ethods o19na'ysis
4 0 9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
UN etail Syllabus o. the Unit
0ene +:pression6Prokaryoti( gene e#pression, operons positi;e B negati;e regu'ation, sigma1a(tors* Initiation, e'ongation and termination o1 trans(ription temp'ate B enFyme properties
2 0enes and +n
-
8/10/2019 bioinformatics semester 8th
9/14
&.!.) SBI0)
Code Course Name Pro, Sem CP CS# SS# Mar)s #ype Cat
I03 Programming in Per' I 4 40 20 00 / .
Course Prereuisites:
Kno'edge o 1 I052, I053,I0%2
Course Ob&ectives: 91ter su((ess1u' (omp'etion o1 this
(ourse, student shou'd e a'e to 8nderstand organisation o1 io'ogi(a' data in
dataases and parse data 1or pro(essing
5emar)s6
UN Name o. Unit CP CS# +valuation Pattern
Per' Introdu(tion B Data /ypes 0 9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
2 .ontro' tru(tures B egu'ar
pressions2 0
9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
3 "ormats 3 0 9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
4 ystem, Netork B D6 using Per' 4 0 9 B @9 in &nd amE and 5 6.s
in e'1-/estE i'' e asked on these units*
UN etail Syllabus o. the Unit
Perl 8ntroduction > ata #ypes6
Introdu(tion B 7;er;ie:
+hat is Per'M +hy use Per' in ioin1ormati(sM istory o1 Per', 9;ai'ai'ity, upport, asi(
.on(epts
(a'ar Data: +hat Is (a'ar DataM, Numers, trings, (a'ar 7perators, (a'ar =aria'es, (a'ar
7perators and "un(tions
9rrays and @ist Data: +hat Is a @ist or 9rrayM @itera' epresentation, =aria'es, 9rray 7perators
and "un(tions, (a'ar and @ist .onte#t
2 Control Structures > 5e,ular +:pressions6
.ontro' tru(tures: tatement 'o(ks
ashes: +hat Is a ashM ash =aria'es, @itera' epresentation o1 a ash, ash "un(tions, ash
'i(es* asi( I$7
egu'ar pressions: .on(epts 9out egu'ar pressions, imp'e 8ses o1 egu'ar pressions,
Patterns, 6ore on t he 6at(hing 7perator, ustitutions, /he sp'it and Coin "un(tions
uroutines: ystem and 8ser "un(tions, /he 'o(a' 7perator, =aria'e-'ength Parameter @ists,
Notes on @e#i(a' =aria'es
6is(e''aneous .ontro' tru(tures:
"i'ehand'es and "i'e /ests: +hat Is a "i'ehand'eM 7pening and .'osing a "i'ehand'e, 8sing
Pathnames and "i'enames, 9 'ight Di;ersion: die, 8sing "i'ehand'es, /he -# "i'e /ests, /he stat
"un(tion
3 -ormats6
+hat Is a "ormatM De1ining a "ormat, In;oking a "ormat
Dire(tory 9((ess: 6o;ing 9round the Dire(tory /ree, G'oing, Dire(tory and'es, 7pening and
.'osing a Dire(tory and'e, eading a Dire(tory and'e
"i'e and Dire(tory 6anipu'ation
Pro(ess 6anagement: 8sing system and e#e(, 8sing a(kAuotes,
7ther Data /rans1ormation: "inding a ustring, tra(ting and ep'a(ing a ustring
"ormatting Data: orting, /rans'iteration
Bio-Informatics Proramme Curriculum Pae ?of 14
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4 System" Net/or) > BM usin, Perl6
ystem In1ormation: Getting 8ser and 6a(hine In1ormation, Pa(king and 8npa(king inary Data
Getting Netork In1ormation
Dataase 6anipu'ation: D6 Dataases and D6 ashes, 7pening and .'osing D6 ashes,
"i#ed-@ength andom-9((ess Dataases, =aria'e-@ength /e#tE Dataases, +in32 Dataase
Inter1a(es
.GI Programming: /he .GI*pm 6odu'e, our .GI Program in .onte#t, imp'est .GI Program,Passing Parameters ;ia .GI, Per' and the +e
7Ce(t oriented per': Introdu(tion to modu'es, .reating 7Ce(ts
ioper': Introdu(tion, Insta''ation pro(edures, 9r(hite(ture, 8ses o1 ioper'
Boo) Code #it le"*uthor"8SBN o. Ori,inal +dition
etails o.Chapters and Sections8ncluded in Syllabus
+dition9ear
Publisher"Price"Order 8t ere
#e:t Boo)s
I03-/ eginning Per' 1or
ioin1ormati(s
>ames /isda'',
In('uded:
('uded:
7-ei''y
I03-/2 De;e'oping ioin1ormati(s.omputer ki''s
.ynthia Gias, Per
>ame(k,
7-ei''y
I03-/3 Programming the Per' DI
9'' igator Des(artes, / im
un(e,
7-ei''y
5e.erence Boo)s
I03- 9d;an(ed Per' Programming
riram rini;asan
7-ei''y
Bio-Informatics Proramme Curriculum Pae 13of 14
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&.!.* SBI0*
Code Course Name Pro, Sem CP CS# SS# Mar)s #ype Cat
I04 Protein t ru(ture Pred i(t ion B
6o'e(u'ar 6ode'ing
I 4 40 20 00 / .
Course Prereuisites:
Kno'edge o1 I05, I0! BI0!4
Course Ob&ectives: 91ter su((ess1u' (omp'etion o1 this(ourse, student shou'd e a'e to
8nderstand ing the ' e;e 's o1 st ru(tureorganiFation o1 ma(romo'e(u'es and re'atedmethods o1 stru(ture determination
8nderstand and use ;arious methods o1 2D and3D stru(ture predi(tion
8nderstand t he inte ra(tion eteenma(romo'e(u'es
5emar)s6
UN Name o. Unit CP CS# +valuation Pattern
Protein Puri.ication 0
9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
2 @ua litative and @uanti tative+valuation o. Protein
2 0 9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
3 +:plorin, proteins3 0
9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
4 Prediction o. Protein Structure4 0
9 B @9 in &nd amE and 5 6.sin e'1-/estE i'' e asked on these units*
UN etail Syllabus o. the Unit
Protein Puri.ication6
asi(s o1 protein puri1i(ation, di11erentia' (entri1ugation, sa'ting out, dia'ysis, ge' 1i'tration and
ion e#(hange (hromatography, a11inity (hromatography, P@., ge' e'e(trophoresis, isoe'e(tri(
1o(using, to dimensiona' e'e(trophoresis*
2 @ualitative and @uantitative +valuation o. Protein6
8'tra(entri1ugation, 6ass spe(tros(opy 69@/DI-/7", peptide mass 1 ingerprinting, eman
degradation, protein seAuen(ing, automated soi'd phase peptide synthesis, N6r spe(tros(opy*
3 +:plorin, proteins6
Dataases:, ND B ..D
.a'(u'ation o1 (on1ormationa' energy 1or io-ma(romo'e(u'es
6o'e(u'ar 6e(hani(s B 6o'e(u'ar Dynami(s o1 7'igopeptides, Proteins, Nu('eotides and sma''
6o'e(u'es
6e(hani(s and dynami(s o1 io-ma(romo'e(u'es
imu'ation o1 mo'e(u'ar me(hani(s and dynami(s
imu'ations o1 "ree &nergy (hanges
"or(e 1ie'ds
6o'e(u'ar intera(tions o1
Protein Protein
Protein DN9
Protein (arohydrate
DN9 sma'' mo'e(u'es et(*
4 Prediction o. Protein Structure6
Predi(tion o1 e(ondary tru(ture using .hou B "asman, G7 series, PD, P6 et(*
Bio-Informatics Proramme Curriculum Pae 11of 14
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6etaser;ers
/ertiary stru(tures o1 Proteins using homo'ogy mode'ing
&;a'uation o1 stru(ture using Pro(he(k, ProsaII et(*
Dataases B ser;ers 1or mode'ing
9pproa(hes ased on Neura'J netorks, geneti( a'gorithms B ma(hine 'earning methods
"o'd re(ognition, threading
6ethods to predi(t three dimensiona' stru(tures o1 nu('ei( a(ids, rN9
.9P, ."9P e#periments
Boo) Code #it le"*uthor"8SBN o. Ori,inal +dition
etails o.Chapters and Sections8ncluded in Syllabus
+dition9ear
Publisher"Price"Order 8t ere
#e:t Boo)s
I04-/ Proteins: tru(ture 9nd
6o'e(u'ar Properties
.reighton, /*&*
In('uded:
('uded:
e(ond&dition
Ne ork* +* *"reeman and .ompany,??3*
I04-/2 Protein "o'ding,*
.reighton,/*
Ne ork* +* *"reeman and .ompany,??2
I04-/3 Protein stru(ture
p red i(t ion: a pra(t i(a'
approa(h, ternerg, 6*>*&*
Ne ork* +* *"reeman and .ompany,??%
I04-/4 6o'e(u'ar mode''ing:
prin(ip'es and app'i(ations
@ea(h* 9* *
5e.erence Boo)s
I04- tru(tura' ioin1ormati(s -
6ethods o 1 io(hemi(a'
9na'ysis =* 44 y Phi'ip &*
ourne &d itorE, e'ge
+eissig &ditorE
+i'ey-@iss, 2003*
Bio-Informatics Proramme Curriculum Pae 12of 14
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8/10/2019 bioinformatics semester 8th
13/14
&.!.+ SBI0+
Code Course Name Pro, Sem CP CS# SS# Mar)s #ype Cat
I05 @a* .ourse I 4 0 20 00 P .
Course Prereuisites:
Kno'edge o1 'ist a'' 4 (ourses in thissem
Course Ob&ectives: 91ter su((ess1u' (omp'etion o1 this
(ourse, student shou'd e a'e to Per1orm pra(t i(a' re'ated to Genomi(
dataases, tru(tura' ioin1ormati(s, GI"P andPer'*
Special Note:tudy .enters shou'd (ondu(t any 23 activitiesout o1 tota' 24 a(ti;ities gi;en in the'ist* tudents are e#pe(ted to per1orm a'' a(ti;ities mentioned in ea(h e#periment and maintain the up-to-date Courna' and get (erti1ied 1rom the 'a instru(tor*
UN etail Syllabus o. the Unit
rosing Genomi( dataases using 6ap=ieer B ensem', ;ieing geneti(, 'inkage maps 1or
human and other mode' organisms*
2 rosing uman genome data, 76I6, NP dataases to understand geneti( and metao'i(
disorders at 'east 2 ea(h
3 rosing genomi( resour(es 1or p'ant, yeast genomes
4 rosing resour(es 1or mi(roia' and ;ira' genomes
5 6ining genomi( data to identi1y genomi( 1eatures: (odon usage, repeats, re;ersa's,
omo'ogous regions, operon stru(tures, synteni( regions, horiFonta' gene trans1er
% Gene predi(tion a'gorithms 1or Prokaryotes at 'east 2E
! Gene predi(tion a'gorithms 1or &ukaryotes at 'east 2E
tru(tura' dataases: re;ise pd, nd, ((sd,
? &;a'uation o1 3D stru(ture o1 proteins:
Pro(he(k, ama(handran p'ot, ProsaII p'ot
0 p'ore: Deri;ed dataases o1 stru(tures: DP, "P, .9/ B .7P
Predi(tion o1 se(ondary stru(tures o1 proteins: at 'east 3 methods 1or 3 proteins
2 Predi(tion o1 /ertiary stru(ture 1o proteins: iss6ode' and 6ode''er
3 p'oring metaser;ers 1or 2D and 3D stru(ture predi(tion
.a'(u'ation o1 6.. B rmsd
4 Identi1ying 1o'd o1 proteins
8se o1 threading ser;ers: Phyre et(
5 &nergy minimisation B geometry optimiFation 1or proteins B peptides
% 8sing ser;ers 1or 1un(tion annotations: &;o'utionary tra(e method et(*
! Per' assignments: !-24
"inding restri(tion ites in gi;en nu('eotide seAuen(e
"inding GI numer 1or a Gi;en 9((ession Numer
? "inding restri(tion ites in gi;en nu('eotide seAuen(e
20 eading "eature ta'e and e#tra(tion o1 seAuen(e position and 1eature in1ormation 1or
ioma(romo'e(u'es*
2 .on;ersion o1 seAuen(e 1ormats
22 Parsing PD 1i'e to popu'ate ta'es in a dataase
23 "inding 6o'e(u'ar eight gi;en the 6o'e(u'ar 1ormu'ae* : .%27%
24 6aking Phy'ogeneti( tree o1 gi;en seAuen(es y using .'usta'+ and P@IP
Bio-Informatics Proramme Curriculum Pae 1$of 14
-
8/10/2019 bioinformatics semester 8th
14/14
Boo) Code #it le"*uthor"8SBN o. Ori,inal +dition
etails o.Chapters and Sections8ncluded in Syllabus
+dition9ear
Publisher"Price"Order 8t ere
#e:t Boo)s
I05-/ ioin1ormati(s9 eginners Guide
.'a;erie, Notredame
In('uded:
('uded:
+i''ey
I05-/2 Programming the Per' DIy 9''igator Des(artes, /imun(e,
7-ei''y*
5e.erence Boo)s
I05- ioin1ormati(s.**=* 6ur thy
ima'aya Pu'ish ingouse
Bio-Informatics Proramme Curriculum Pae 14of 14