‫ قواعد البيانات الحيوية‬  

9:00-11:00

15/1/2022
‫سارة صلاح محمد‬/‫
د‬
Faculty of Computers & Information, Assiut University

4th Level

Final Exam

Duration: 2 hours

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(‫* الإسم الرباعي (بالعربي فقط‬

‫* رقم الجلوس‬

1/13/2022
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‫* المستوي‬

‫الاول‬

‫الثاني‬

‫الثالث‬

‫الرابع ‪2013‬‬

‫الرابع ‪2014‬‬

‫الرابع ‪2015‬‬

‫الرابع ‪2016‬‬

‫الرابع ‪2017‬‬

‫الرابع ‪2018‬‬

‫‪4‬‬

‫* البرنامج‬

‫عام‬

‫بايو‬

‫هندسة‬

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‫* رقم الصالة‬

‫أ_‪1‬‬

‫أ_‪2‬‬

‫أ_‪3‬‬

‫أ_‪4‬‬

‫أ_‪5‬‬

‫ج_‪1‬‬

‫ج_‪2‬‬

‫ج_‪3‬‬

‫ج_‪4‬‬

‫ج_‪5‬‬

‫ج_‪6‬‬

‫‪6‬‬

‫* رقم الكمبيوتر‬

‫‪7‬‬

‫* الكود (قد تمت مراجعة بيانات الطالب ورقم الجلوس(‬

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 8

In a protein sequence alignment, _________ refers to the percentage of matches of the

same amino acid residues between two aligned sequences.
(1 Point)

a) Sequence identity

b) Sequence homology

c) Sequence similarity

d) Sequence non homology

Suitable for aligning more divergent sequences or distantly related sequences

__________________

(1 Point)

a) Global alignments

b) Local alignments

10

Biopython has full support for the querying of the KEGG api.
(1 Point)

a) True

b) False

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 11

Homologous sequences are ___________if they were separated by a speciation event:

when a species diverges into two separate species.
(1 Point)

a) paralogous

b) orthologous

12

This function returns basic information about a specified `KEGG` database -

much like visiting the landing page for that database.
(2 Points)

a) kegg_link() 

b) kegg_list()

c) kegg_info()

13

What is the correct line to  get coding sequence for KSE_17560 ?
(2 Points)

a) result = REST.kegg_get("ksk:KSE_17560", "aaseq").read()

b) result = REST.kegg_get("ksk:KSE_17560", "ntseq").read()

c) none of the above

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 14

FlyBae is a ______
(1 Point)

a) Biodiversity database

b) Model organism database

c) Literature database

d) Biomolecular database

15

Among the following which one is not the approach to the local alignment?

(1 Point)

a) Smith-Waterman algorithm

b) K-tuple method

c) Words method

d) Needleman-Wunsch algorithm

16

Prosite is a database containing protein domains, protein families, functional sites, as

well as the patterns and profiles to recognize them
(1 Point)

a) True

b) False

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 17

 A problem exists when comparing _____ sequences using the dot matrix method,
namely, the _______

(1 Point)

a) small, amplification

b) large, amplification

c) small, high noise level

d) large, high noise level

18

ScanProsite allows you to scan protein sequences online against the Prosite database
by providing _____
(1 Point)

a) UniProt sequence identifier

b) PDB sequence identifier

c) The sequence itself.

d) All of the above.

19

If you do not have the  accession number or entry name  of orchid proteins for
Chalcone Synthase you can't use get_sprot_raw() function of Bio.ExPASy to extract
records.
(1 Point)

a) True

b) False
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 20

Despite the obvious drawbacks of using flat files in database management, many
biological databases still use this format.
(1 Point)

a) True

b) False

21

Which of the following does not describe BLOSUM matrices?

(1 Point)

a) It stands for BLOcks SUbstitution Matrix

b) It was developed by Henikoff and Henikoff

c) The year it was developed was 1992

d) These matrices are logarithmic identity values

22

When the two sequences have substantial regions of similarity, many dots line up to
form contiguous _______ lines.

(1 Point)

a) crossings on

b) horizontal

c) diagonal

d) vertical

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 23

 The heterogeneous database structures does not limit communication between

databases.
(1 Point)

a) True

b) False

24

One of the databases accessible from Entrez is a biomedical literature database

known as
(1 Point)

a) PIR

b) Swiss prot

c) PubMed

25

There are two ways to search for sequences in GenBank.

(1 Point)

a) True

b) False

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 26

The GenBank Sequence file contain two sections – Header and Sequence entry
(1 Point)

a) True

b) False

27

Sequence alignment can not be used as basis for prediction of structure and function
of

uncharacterized sequences.
(1 Point)

a) True

b) False

28

_________It is useful in identifying chromosomal repeats and in comparing gene order

conservation between two closely related genomes.
(1 Point)

a) Smith-Waterman method

b) Dot matrix method

c) Needleman-Wunsch method

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 29

Scope is ____

(1 Point)

a) Structure database

b) Gene expression database

30

What is the output of the following code ?

>>> sequence = "MEHKEVVLLLLLFLKSGQGEPL "

>>> from Bio.ExPASy import ScanProsite

>>> handle = ScanProsite.scan(seq=sequence)

>>> result = ScanProsite.read (http://scanprosite.read)(handle)

>>> len(result)

(1 Point)

a) Number of search sequences

b) Number of hits

c) Error

31

Prosite is an  example  of _____

(1 Point)

a) Primary databases.

b) Secondary databases

c) Specialized databases

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 32

Does the code below  find all shiga toxin genes?

result = REST.kegg_find("compound", "shiga+toxin").read()

to_df(result)

(2 Points)

a) True

b) False

33

 The function get_prosite_entry() is used to download the Prosite documentation

records in HTML format
(1 Point)

a) True

b) False

34

Which of the following is incorrect regarding sequence homology?

(1 Point)

a) Two sequences can homologous relationship even if have do not have common origin

b) It is an important concept in sequence analysis

c) When two sequences are descended from a common evolutionary origin, they are said to have a
homologous relationship

d) When two sequences are descended from a common evolutionary origin, they are said to share
homology

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 35

To parse a Swiss-Prot file, you write in the code

>>> from Bio import SwissProt

>>> handle = open("myfile.dat")

 >>> records = SwisProt.read (http://swisprot.read) (handle)

(1 Point)

a) True

b) False

36

 __________is a database that provides all the information about the human
inheritance.
(1 Point)

a) PDB

b) STAG

c) OMIM

37

The following code written to get a list of all human pathways, complete the missing
part

from Bio.KEGG import REST

human_pathways = REST.kegg_list("???", "???").read()

(1 Point)

pathway,hsa

pathway,mmu

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 38

To see the members of a Swiss-Prot record?

(1 Point)

a) list(record)

b) dir(record)

c) next(records)

d) none of the above

39

If you have keywlist.txt file, which lists the keywords and categories used in Swiss-
Prot.

To print the description of each record you write the code

(1 Point)

a) print(record["ID"])

b) print(record.ID (http://record.ID))

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 40

The code to read an Enzyme file containing two Enzyme records is?

>>> from Bio.ExPASy import Enzyme

>>> with open("lipoprotein.txt") as handle:

    record = Enzyme.read (http://enzyme.read)(handle)

(1 Point)

a) True

b) False

41

_____________is a comprehensive proteomics web server with a suite of programs for

searching peptide information from the SWISS-PROT and TrEMBL databases.

(1 Point)

a) ExPASY

b) Prosite

c) None of the above

42

In Smith–Waterman algorithm, to align two sequences of lengths of m and n

_________ time is required.

(1 Point)

a) O(mn)

b) O(m2n)

c) O(m2n3)

d) O(mn2)
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 43

Traceback the alignment in the figure. When the scoring matrix is 1 for Match and -1
for Mismatch and gap penalty=-2   what is the alignment?
(2 Points)

GTCGACGCA| GATTAC__A

G_TCGACGCA| GATTAC___A

GTCCACGCA| GATTAC__A

None of the above

44

When you use Needleman-Wunsch algorithm to align two identical sequences, the

length of sequence is n and  the scoring matrix is 2 for Match and -2 for Mismatch
and gap penalty=-4,   what is the score?
(2 Points)

n-2

n-1

2n

none of the above

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 45

One of the problems with relational databases is that the tables used do not describe
complex hierarchical relationships between data items
(1 Point)

a) True

b) False

46

Redundancy is one of the major problems affecting primary databases.

(1 Point)

a) False

b) True

47

Homologous sequences are ____________ if they were separated by a gene duplication

event.

(1 Point)

a) orthologous

b) paralogous

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 48

Margaret Oakley Dayhoff developed the first protein sequence database called

(1 Point)

a) SWISS-PROT

b) Atlas of protein sequence and structure 

c) PDB

49

For palindromic sequences, what is the structure of the dot plot?

(2 Points)

a) 2 intersecting diagonal lines at the midpoint

b) One diagonal

c) Two parallel diagonals

d) No diagonal

50

All the following are protein sequence database except? ______

(1 Point)

a) PIR

b) Swiss prot

c) EMBL

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 51

GenBank, the nucleic acid sequence database is maintained by ________

(1 Point)

a) DDBJ

b) EMBL

c) NCBI

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