SIX1008 BIOCOMPUTING

SEMESTER I, ACADEMIC SESSION 2019/2020

SIX1008 BIOCOMPUTING
GROUP PROJECT

GROUP: 1

SEMESTER: 1

ACADEMIC SESSION: 2019/2020

COURSE INSTRUCTOR: ASSOCIATE PROFESSOR DR. TEOH TEOW CHONG

DEADLINE: 27th of December, 2019

TEAM MEMBERS

NAME MATRIC NUMBER

1. NUR ATIKAH BINTI AZALI SIF160058

2. AMIRAH BINTI BASIR SIF170004

3. MAISARAH BINTI SAIHUN SIF170017

4. LIM CHI CHING SIQ170012

5. PUA WEI YI SIP180017

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1. Compute the pair sequence alignment using generalGap.py and localAlign.py scripts for the
following sequences: [10 marks]

a) RNASEQUENCE

CONSEQUENCE

generalGap.py

localAlign.py

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b) CONSIGNMENT

ASSIGNMENT

generalGap.py

localAlign.py

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c) SIMILAR

SINGULAR

generalGap.py

localAlign.py

d) THISISTHETHESIS

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HYPOTHESIS

generalGap.py

localAlign.py

e) AFFINITY

IDENTITY
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generalGap.py

localAlign.py

2. By using the Protein BLAST at https://blast.ncbi.nlm.nih.gov/Blast.cgi, perform the local

sequence alignment for the amino acid sequences below, and identify the proteins. [10 marks]

>Q1

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ADLELERAADVRWEEQAEISGSSPTLSITISEDGSMSIKNEEEEQTLGGGGTGGGGAGVLWDVP
SPPPVGKAELEDGAYRIKQKGILGYSQIGAGVYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADK
KDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNTGTIGAVSLDFSPGTSGS
PIVDKKGKVVGLYGNGVVTRSGTYVSAIAQTERSIEDNPEIEDDIFRKRKL

A) Protein Identified: Chain A, FLAVIVIRUS_NS2B/Peptidase S7 [Dengue virus 2]

Score 466 bits (1199)

Expect 2e-165

Method Compositional matrix adjust.

Identities 235/241 (98%)

Positives 237/241 (98%)

Gaps 1/241 (0%)

B) Protein Identified: Chain A, Ns2b-ns3 Protease [Dengue virus 2]

Score 466 bits (1198)

Expect 2e-165

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Method Compositional matrix adjust.

Identities 235/241 (98%)

Positives 237/241 (98%)

Gaps 1/241 (0%)

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C) Protein Identified: Chain A, Ns2b-ns3 Protease [Dengue virus 2]

Score 465 bits (1196)

Expect 6e-165

Method Compositional matrix adjust.

Identities 234/241 (97%)

Positives 236/241 (97%)

Gaps 1/241 (0%)

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>Q2

GSHMVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEDDGPPMAGGGGSGGGGSGAL
WDVPAPKEVKKGETTDGVYRVMTRGLLGSTQVGVGVMQEGVFHTMWHVTKGSALRSGEGRLDPY
WGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARNIQTLPGIFKTKDGDIGAVALDYPA
GTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGRR

A) Protein Identified: Chain A, Ns2b-ns3 Protease, ns2b-ns3 Protease [Zika virus]

Score 461 bits (1187)

Expect 4e-164

Method Compositional matrix adjust.

Identities 230/230 (100%)

Positives 230/230 (100%)

Gaps 0/230 (0%)

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B) Protein Identified: Chain A, Ns2b-ns3 Protease Chimera, genome Polyprotein

[Zika virus]

Score 450 bits (1158)

Expect 2e-159

Method Compositional matrix adjust.

Identities 224/226 (99%)

Positives 225/226 (99%)

Gaps 0/226 (0%)

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>Q3

GSVVIVGRIILGSGSAPITAYAQQTRGLFGTIVTSLTGRDKNVVTGEVQVLSTATQTFLGTTVG
GVMWTVYHGAGSRTLAGTKHPALQMYTNVDQDLVGWPAPPGAKSLEPCTCGSADLYLITRDADV
IPARRRGDSTASLLSPRPLACLKGSSGGPVMCPAGHVAGIFRAAVCTRGVAKALQFIPVETLST
QARS

A) Protein Identified: protease-helicase, partial [Hepacivirus C]

Score 363 bits (931)

Expect 2e-126

Method Compositional matrix adjust.

Identities 178/181 (98%)

Positives 180/181 (99%)

Gaps 0/181 (0%)

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B) Protein Identified: protease-helicase, partial [Hepacivirus C]

Score 362 bits (930)

Expect 3e-126

Method Compositional matrix adjust.

Identities 177/181 (98%)

Positives 180/181 (99%)

Gaps 0/181 (0%)

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C) Protein Identified: NS3 protease, partial [Hepacivirus C]

Score 362 bits (930)

Expect 3e-126

Method Compositional matrix adjust.

Identities 177/181 (98%)

Positives 180/181 (99%)

Gaps 0/181 (0%)

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>Q4

TDMWLERAADISWEMDAAITGSSRRLDVKLDDDGDFHLIDDPGVPWKGGGGSGGGGGGVFWDTP
SPKPCSKGDTTTGVYRIMARGILGTYQAGVGVMYENVFHTLWHTTRGAAIMSGEGKLTPYWGSV
KEDRIAYGGPWRFDRKWNGTDDVQVIVVEPGKAAVNIQTKPGVFRTPFGEVGAVSLDYPRGTSG
SPILDSNGDIIGLYGNGVELGDGSYVSAIVQGDRQEEPVPEAYT

A) Protein Identified: polyprotein, partial [Japanese encephalitis virus]

Score 447 bits(1151)

Expect 5e-151

Method Compositional matrix adjust.

Identities 227/262(87%)

Positives 228/262(87%)

Gaps 26/262(9%)

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B) Protein Identified: polyprotein [Japanese encephalitis virus]

Score 456 bits(1173)

Expect 3e-144

Method Compositional matrix adjust.

Identities 229/262(87%)

Positives 229/262(87%)

Gaps 26/262(9%)

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C) Protein Identified: polyprotein [Japanese encephalitis virus]

Score 454 bits(1169)

Expect 1e-143

Method Compositional matrix adjust.

Identities 228/262(87%)

Positives 228/262(87%)

Gaps 26/262(9%)

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>Q5

TDMWIERTADITWESDAEITGSSERVDVRLDDDGNFQLMNDPGAPWKGGGGSGGGGGGVLWDTP
SPKEYKKGDTTTGVYRIMTRGLLGSYQAGAGVMVEGVFHTLWHTTKGAALMSGEGRLDPYWGSV
KEDRLCYGGPWKLQHKWNGHDEVQMIVVEPGKNVKNVQTKPGVFKTPEGEIGAVTLDYPTGTSG
SPIVDKNGDVIGLYGNGVIMPNGSYISAIVQGERMEEPAPAGFEPEMLR

A) Protein Identified: CF40GlyNS3pro protein [synthetic construct]

Score 475 bits(1223)

Expect 5e-169

Method Compositional matrix adjust.

Identities 234/240(98%)

Positives 238/240(99%)

Gaps 0/240(0%)

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B) Protein Identified: Chain A, Serine Protease Subunit Ns2b, Serine Protease Ns3
[West Nile virus]

Score 454 bits(1169)

Expect 4e-161

Method Compositional matrix adjust.

Identities 225/226(99%)

Positives 225/226(99%)

Gaps 0/226(0%)

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C) Protein Identified: NS2-NS3 protein [West Nile virus]

Score 469 bits(1206)

Expect 2e-159

Method Compositional matrix adjust.

Identities 232/267(87%)

Positives 232/267(86%)

Gaps 26/267(9%)

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3. Download a protein databank (pdb) file for HIV-1 gp120-CD4 protein structure at
https://www.rcsb.org/, by using molecular viewer of RasWin, print the molecular rendering for:
[5 marks]

a) Wireframe

b) Sticks

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c) Spacefill

d) Ball & Stick

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e) Cartoons

Due date: 27/12/2019, Friday

Format: Hardcopy submitted to Ms. Devi.

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