Assiut University
Faculty of Computers and
Information
Course Code:BNF424
Course Name: Biological Databases
4th Level
Questions Bank
Choose the correct answer:
1) All the following are proteinsequence databaseexcept? ______
a) PIR
b) Swiss prot
c) EMBL
2) __________is a database that provides all the information about the human
inheritance.
a) PDB
b) STAG
c) OMIM
3) GenBank, the nucleic acid sequence database is maintained by ________
a) DDBJ
b) EMBL
c) NCBI
4) FlyBae is a ______
a) Biodiversity database
b) Model organism database
c) Literature database
d) Biomolecular database
5) To parse a Swiss-Prot file, you write in the code
>>> from Bio import SwissProt
>>> handle = open("myfile.dat")
>>> records = SwissProt.read (handle)
a) True
b) False
6) CDS field in the GenBank files contains _____:
a) Information about the boundaries of the sequence that can be translated into
amino acids.
b) Accession number for the sequence
7) The global sequence alignment for the two sequences
V=TGGTG , W=ATCGT .When the scoring matrix is 1 for Match and -1 for
Mismatch and gap penalty=-2 is – T G G T G , A T C G T –.
a) True
b) False
8) The score of the pervious alignment is equal to ____
a) -2
b) -3
c) -1
9) Progenitor sequences represented by the ______ branches of the tree are
derived by alignment of the _______ sequences.
a) outer, outermost
b) inner, outermost
c) inner, innermost
d) outer, innermost
10) To parse a Prosite file, you write in the code
>>> from Bio import SwissProt
>>> handle = open("myprositefile.dat")
>>> records = Prosite.parse(handle)
a) True
b) False
11) In Smith–Waterman algorithm, in initialization Step, the _________ row and
________ column are subject to gap penalty.
a) first, first
b) first, second
c) second, First
d) first, last
12) In SW algorithm, to align two sequences of lengths of m and n _________
time is required.
a) O(mn)
b) O(m2n)
c) O(m2n3)
d) O(mn2)
13)
TrEMBL consists of entries in the same format as SWISS-PROT.
a) True
b) False
14) Many studies have demonstrated that the distribution of similarity scores
assumes a peculiar shape that resembles a highly skewed normal distribution
with a long tail on one side. The distribution matches the _______
a) Gumble elective value distribution
b) Gumble extreme void distribution
c) Gumble end value distribution
d) Gumble extreme value distribution
15) ExPASY is a comprehensive proteomics web server with a suite of programs
for searching peptide information from the SWISS-PROT and TrEMBL
databases.
a) True
b) False
16) The rigorous dynamic programming method is normally not used for
database searching because it is slow and computationally expensive.
a) True
b) False
17) Which of the following does not describe local alignment algorithm?
a) Score can be negative
b) Negative score is set to 0
c) First row and first column are set to 0 in initialization step
d) In traceback step, beginning is with the highest score, it ends when 0 is
encountered
18) a Prosite file can contain more than one Prosite records
a) True
b) False
19) Local alignments are more used when _____________
a) There are totally similar and equal length sequences
b) Dissimilar sequences are suspected to contain regions of similarity
c) Similar sequence motif with larger sequence context
d) Partially similar, different length and conserved region containing sequences
20)
Which of the following does not describe BLOSUM matrices?
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
21) In a dot matrix, two sequences to be compared are written in the
_____________ of the matrix.
a) horizontal and vertical axes
b) 2 parallel horizontal axes
c) 2 parallel vertical axes
d) horizontal axis (one preceding another)
22) Among the following which one is not the approach to the local alignment?
a) Smith-Waterman algorithm
b) K-tuple method
c) Words method
d) Needleman-Wunsch algorithm
23) Which of the following does not describe BLAST?
a) It stands for Basic Local Alignment Search Tool
b) It uses word matching like FASTA
c) It is one of the tools of the NCBI
d) Even if no words are similar, there is an alignment to be considered
24) Which of the following is incorrect regarding pair wise sequence alignment?
a) The most fundamental process in this type of comparison is sequence
alignment
b) It is an important first step toward structural and functional analysis of newly
determined sequences
c) This is the process by which sequences are compared by searching for
common character patterns and establishing residue-residue correspondence
among related sequences
d) It is the process of aligning multiple sequences
25)
Which of the following is incorrect about ENTREZ?
a) It is a resource prepared only by the staff of the National Center for
Biotechnology Information
b) It provides a series of forms that can be filled out to retrieve a Medline
reference related to the molecular biology sequence databases
c) One straightforward way to access the sequence databases is through
ENTREZ
d) It provides a series of forms that can be filled out to retrieve a DNA or
protein sequence
26) SWISS-PROT is a repository for ____________
a) Nucleotide sequences
b) Protein sequences
c) Vectors
d) Genome arrays
27) Prosite is a database containing protein domains, protein families, functional
sites, as well as the patterns and profiles to recognize them
a) True
b) False
28)
Which of the following is incorrect about evolution?
a) The macromolecules can be considered molecular fossils that encode the
history of millions of years of evolution
b) The building blocks of these biological macromolecules, nucleotide bases,
and amino acids form linear sequences that determine the primary structure of
the molecules
c) DNA and proteins are products of evolution
d) The molecular sequences barely undergo changes
29) If the two sequences share significant similarity, it is extremely ______ that
the extensive similarity between the two sequences has been acquired
randomly, meaning that the two sequences must have derived from a common
evolutionary origin.
a) unlikely
b) possible
c) likely
d) relevant
30) Which of the following is incorrect regarding sequence homology?
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
31) When the two sequences have substantial regions of similarity, many dots
line up to form contiguous _______ lines.
a) crossings on
b) horizontal
c) diagonal
d) vertical
32)
A problem exists when comparing _____ sequences using the dot matrix
method, namely, the _______
a) small, amplification
b) large, amplification
c) small, high noise level
d) large, high noise level
33)
In local alignment, the two sequences to be aligned cannot be of unequal
lengths.
a) True
b) False
34)
Alignment algorithms, both global and local, are fundamentally similar and
only differ in the optimization strategy used in aligning similar residues.
a) True
b) False
35)
Self complementarity of DNA sequences cannot be identified using a dot
plot.
a) True
b) False
36)
A sequence can be aligned with itself to identify internal repeat elements.
a) True
b) False
37)
The truly statistically significant sequence alignment will be able to provide
evidence of homology between the sequences involved.
a) True
b) False
38) Score can be negative in Smith–Waterman algorithm.
a) True
b) False
39) The function of the scoring matrix is to conduct one-to-one comparisons
between all components in two sequences and record the optimal alignment
results.
a) True
b) False
40) KEGG is a database resource for understanding high-level functions and
utilities of the biological system, such as the cell, the organism and the
ecosystem
a) True
b) False