Granting agency requires a certain level of accuracy in case of errors. Which of the given statements is untrue regarding it?

Base insertions/deletions will cause frame-shifts in the sequence

In other laboratories, such as those performing a single-attempt sequencing of ESTs, the error rate may be much higher, approximately 1 in 100, including incorrectly identified bases and inserted or deleted bases

Incorrect bases always translate to the right amino acid

Base insertions/deletions will cause frame-shifts in the sequence

Making alignment with a protein sequence becomes difficult because of frameshifts

Which of the following is untrue about Shotgun Sequencing?

In a new whole shotgun approach, Celera Genomics is sequencing both ends of DNA fragments of short (2 kb), medium (10 kb), and long (BAC or >100 kb) lengths

When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to overlap

When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to scrutinize

In a new whole shotgun approach, Celera Genomics is sequencing both ends of DNA fragments of short (2 kb), medium (10 kb), and long (BAC or >100 kb) lengths

A large number of reads are then assembled by computer

Which of the given statements is incorrect about READSEQ?

It is an extremely useful sequence formatting program developed by D. G. Gilbert at Indiana University, Bloomington

It was developed at Indiana University, Bloomington

It can recognize a DNA or protein sequence file in any of the formats

It can recognize a DNA or protein sequence file in some particular formats

Which of the given statements is incorrect about Block multiple sequence alignment format?

AC contains the block number, a seven-character group number for sequences from which the block was made, followed by a letter (A–Z) indicating the order of the block in the sequences

Identification starts contain a short identifier for the group of sequences from which the block was made and often is the original Prosite group ID

The identifier is terminated by a comma, and “BLOCK” indicates the entry type

AC contains the block number, a seven-character group number for sequences from which the block was made, followed by a letter (A–Z) indicating the order of the block in the sequences

The block number is a 5-digit number preceded by BL (BLOCKS database) or PR (PRINTS database)

Which of the given statements is untrue?

ASCII and binary modes cannot be set by the user

Sequence and other data files that contain non-ASCII characters also may not be transferred correctly from one machine to another and may cause unpredictable behavior of the communications software

The ASCII mode is useful for transferring text files, and the binary mode is useful for transferring compressed data files, which also contain non-ASCII characters

ASCII and binary modes cannot be set by the user

Most sequence analysis programs also require not only that a DNA or protein sequence file be a standard ASCII file, but also that the file be in a particular format such as the FASTA format

Which of the given statements is incorrect?

Editing a sequence file with a word processor can introduce such changes if one is not careful to work only with text or so-called ASCII files

Before using a sequence file in a sequence analysis program, it is important to ensure that computer sequence files contain only sequence characters and not special characters used by text editors

Computer sequence files might contain special characters used by text editors

Editing a sequence file with a word processor can introduce such changes if one is not careful to work only with text or so-called ASCII files

Most text editors normally create text files that include control characters in addition to standard ASCII characters

Which of the given statements is incorrect about ASCII and Hexadecimal?

Each character is stored in binary code in the smallest unit of memory, called a bit

Computers store sequence information as simple rows of sequence characters called strings, which are similar to the sequences shown on the computer terminal

Each character is stored in binary code in the smallest unit of memory, called a byte

Each character is stored in binary code in the smallest unit of memory, called a bit

By convention, many of these combinations have a specific definition, called their ASCII equivalent

Which of the following is wrong about FASTA Sequence Format?

The FASTA sequence format includes a comment line identified by a “>” character in the first column followed by the name and origin of the sequence

The FASTA sequence format includes the sequence in standard one-letter symbols

This format provides a very convenient way to copy just the sequence part from one window to another because there are no numbers or other nonsequence characters within the sequence

The presence of ‘*’ is not quite essential for reading the sequence correctly by some sequence analysis programs

Which of the following is wrong about Abstract Syntax Notation Sequence Format?

The information is much more difficult to read by eye than a GenBank formatted sequence

Abstract Syntax Notation (ASN.1) is a formal data description language that has been developed by the computer industry

All the information found in other forms of sequence storage, e.g., the GenBank format, is present. For example, sequences can be retrieved in this format by ENTREZ

Taxonomic information and bibliographic information cannot be encoded with this format

Which of the following is wrong about National Biomedical Research Foundation/Protein Information Resource Sequence Format?

The first line includes an initial “>” character followed by a two-letter code such as P for complete sequence or F for fragment, followed by a 1 or 2 to indicate type of sequence, then a semicolon, then a four- to six-character unique name for the entry

Sequences retrieved from the PIR database are not in this compact format, but in an expanded format with much more information about the sequence

The NBRF format is similar to the FASTA sequence format but with significant differences

This is different than PIR format

The first line includes an initial “>” character followed by a two-letter code such as P for complete sequence or F for fragment, followed by a 1 or 2 to indicate type of sequence, then a semicolon, then a four- to six-character unique name for the entry

Which of the following is wrong about Genetics Computer Group Sequence Format?

If one or more sequence characters become changed through error, a program reading the sequence will be able to determine that the change has occurred because the checksum value in the sequence entry will no longer be correct

Earlier versions of the Genetics Computer Group (GCG) programs require a unique sequence format and include programs that convert other sequence formats into GCG format

Information about the sequence in the GenBank entry is not included but the line information is carried out

If one or more sequence characters become changed through error, a program reading the sequence will be able to determine that the change has occurred because the checksum value in the sequence entry will no longer be correct

Lines of information are terminated by two periods, which mark the end of information and the start of the sequence on the next line

Which of the following is wrong about European Molecular Biology Laboratory Data Library Format?

Information is organized into fields, each with an identifier, shown as the first text on each line

EMBL maintains DNA and protein sequence databases

As with GenBank entries, a large amount of information describing each sequence entry is given

Sequence entry includes literature references and information about the function of the sequence, but not locations of mRNAs and coding regions

Information is organized into fields, each with an identifier, shown as the first text on each line

Which of the following is wrong about GenBank DNA Sequence Entry?

The information is organized into fields, each with an identifier, shown as the first text on each line

In some entries, these identifiers may be abbreviated to two letters, e.g., RF for reference

Some identifiers may have additional subfields

The CDS subfield in the field FEATURES does not offer the amino acid sequence

Which of the following is incorrect about ENTREZ?

It provides a series of forms that can be filled out to retrieve a Medline reference related to the molecular biology sequence databases

It is a resource prepared only by the staff of the National Center for Biotechnology Information

It provides a series of forms that can be filled out to retrieve a Medline reference related to the molecular biology sequence databases

One straightforward way to access the sequence databases is through ENTREZ

It provides a series of forms that can be filled out to retrieve a DNA or protein sequence

Which of the given statements is incorrect about global gene regulation?

Cell cycle is a developmental phase, or a response to the environment

One way to obtain useful information about a genome is to determine which genes are induced or repressed in response to a phase of the cell cycle

Sets of a gene whose expression rises and falls under the same condition are likely to have a related function

Sets of a gene whose expression rises and falls under the same condition are likely to have dissimilar functions

Cell cycle is a developmental phase, or a response to the environment

Which of the given statement is incorrect about proteome analyses?

For BLAST, setting an effective database size appropriate for each search and program is important

Due to the large number of comparisons that must be made in these types of analyses and due to the volume of program output, the procedure must be automated on a local machine using Perl scripts or a similar method and a database system

BLAST is used for obtaining a correct statistical evaluation of alignment scores

BLAST does not give statistical evaluation of alignment scores

Which of the given statements is incorrect about Family and Domain Analysis?

Comparison of the domain content of an entire proteome with that of another proteome cannot help in revealing the biological roles of diverse domains in different organisms

Gene identification of predicted proteins in the genome is designed to discover the metabolic features of an organism

In a particular organism or group of organisms, one particular domain can be expanded to perform a particular function

Comparison of the domain content of an entire proteome with that of another proteome cannot help in revealing the biological roles of diverse domains in different organisms

Different proteins are mosaics of domains that occur in different combinations in a given protein

Which_of_the_following_is_untrue_about_Shotgun_Sequencing?$

In a new whole shotgun approach, Celera Genomics is sequencing both ends of DNA fragments of short (2 kb), medium (10 kb), and long (BAC or >100 kb) lengths

When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to overlap

When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to scrutinize

In a new whole shotgun approach, Celera Genomics is sequencing both ends of DNA fragments of short (2 kb), medium (10 kb), and long (BAC or >100 kb) lengths

A large number of reads are then assembled by computer

156 + Mcqs in Dna Genomic Sequencing in Bioinformatics Page 3 McqOptions

101.	Granting agency requires a certain level of accuracy in case of errors. Which of the given statements is untrue regarding it?
A.	In other laboratories, such as those performing a single-attempt sequencing of ESTs, the error rate may be much higher, approximately 1 in 100, including incorrectly identified bases and inserted or deleted bases
B.	Incorrect bases always translate to the right amino acid
C.	Base insertions/deletions will cause frame-shifts in the sequence
D.	Making alignment with a protein sequence becomes difficult because of frameshifts
Answer» C. Base insertions/deletions will cause frame-shifts in the sequence

102.	NCBI reviews new entries and updates existing ones, as requested.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

103.	Once the correct map has been obtained, unique overlapping clones are chosen for sequencing.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

104.	An alternative method is to sequence all the subclones, produce a computer database of the sequences, and then have the computer assemble the sequences from the overlaps that are found.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

105.	Which of the following is untrue about Shotgun Sequencing?
A.	When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to overlap
B.	When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to scrutinize
C.	In a new whole shotgun approach, Celera Genomics is sequencing both ends of DNA fragments of short (2 kb), medium (10 kb), and long (BAC or >100 kb) lengths
D.	A large number of reads are then assembled by computer
Answer» C. In a new whole shotgun approach, Celera Genomics is sequencing both ends of DNA fragments of short (2 kb), medium (10 kb), and long (BAC or >100 kb) lengths

106.	Which of the given statements is incorrect about READSEQ?
A.	It is an extremely useful sequence formatting program developed by D. G. Gilbert at Indiana University, Bloomington
B.	It was developed at Indiana University, Bloomington
C.	It can recognize a DNA or protein sequence file in any of the formats
D.	It can recognize a DNA or protein sequence file in some particular formats
Answer» E.

107.	BL contains information about the block: xxx is the amino acids in the spaced triplet found by MOTIF upon which the block is based.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

108.	Which of the given statements is incorrect about Block multiple sequence alignment format?
A.	Identification starts contain a short identifier for the group of sequences from which the block was made and often is the original Prosite group ID
B.	The identifier is terminated by a comma, and “BLOCK” indicates the entry type
C.	AC contains the block number, a seven-character group number for sequences from which the block was made, followed by a letter (A–Z) indicating the order of the block in the sequences
D.	The block number is a 5-digit number preceded by BL (BLOCKS database) or PR (PRINTS database)
Answer» C. AC contains the block number, a seven-character group number for sequences from which the block was made, followed by a letter (A–Z) indicating the order of the block in the sequences

109.	Data files that have multiple sequences, such as those required for multiple sequence alignment and phylogenetic analysis using parsimony (PAUP), are not converted in READSEQ.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

110.	The “from” programs convert sequence files from GCG format into the named format, and the “to” programs convert the alternative format into GCG format.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

111.	Which of the given statements is untrue?
A.	Sequence and other data files that contain non-ASCII characters also may not be transferred correctly from one machine to another and may cause unpredictable behavior of the communications software
B.	The ASCII mode is useful for transferring text files, and the binary mode is useful for transferring compressed data files, which also contain non-ASCII characters
C.	ASCII and binary modes cannot be set by the user
D.	Most sequence analysis programs also require not only that a DNA or protein sequence file be a standard ASCII file, but also that the file be in a particular format such as the FASTA format
Answer» C. ASCII and binary modes cannot be set by the user

112.	According to standard amino acid code letters which of the given pair is not right?
A.	K- lysine
B.	Y- tyrosine
C.	Q- glutamine
D.	R- serine
Answer» E.

128.	In Reverse-genetics analysis of gene function– Even though a particular gene may be _____ ortholog of a gene of known function in another organism, that gene may be acquired by a _____ function.
A.	a highly predicted, similar
B.	a highly predicted, same
C.	a highly predicted, novel
D.	less predicted, novel
Answer» D. less predicted, novel

134.	Using boolean logic, the search looks for database entries that include the first term __________ the second, and subsequent terms repeated until the last term.
A.	AND
B.	OR
C.	ExOR
D.	NAND
Answer» B. OR

113.	For computer analysis of proteins, it is more convenient to use single-letter than three letter amino acid codes.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

114.	Which of the given statements is incorrect?
A.	Before using a sequence file in a sequence analysis program, it is important to ensure that computer sequence files contain only sequence characters and not special characters used by text editors
B.	Computer sequence files might contain special characters used by text editors
C.	Editing a sequence file with a word processor can introduce such changes if one is not careful to work only with text or so-called ASCII files
D.	Most text editors normally create text files that include control characters in addition to standard ASCII characters
Answer» C. Editing a sequence file with a word processor can introduce such changes if one is not careful to work only with text or so-called ASCII files

115.	Which of the given statements is incorrect about ASCII and Hexadecimal?
A.	Computers store sequence information as simple rows of sequence characters called strings, which are similar to the sequences shown on the computer terminal
B.	Each character is stored in binary code in the smallest unit of memory, called a byte
C.	Each character is stored in binary code in the smallest unit of memory, called a bit
D.	By convention, many of these combinations have a specific definition, called their ASCII equivalent
Answer» C. Each character is stored in binary code in the smallest unit of memory, called a bit

116.	Which of the following is wrong about FASTA Sequence Format?
A.	The FASTA sequence format includes a comment line identified by a “>” character in the first column followed by the name and origin of the sequence
B.	The FASTA sequence format includes the sequence in standard one-letter symbols
C.	This format provides a very convenient way to copy just the sequence part from one window to another because there are no numbers or other nonsequence characters within the sequence
D.	The presence of ‘*’ is not quite essential for reading the sequence correctly by some sequence analysis programs
Answer» E.

117.	Which of the following is wrong about Abstract Syntax Notation Sequence Format?
A.	The information is much more difficult to read by eye than a GenBank formatted sequence
B.	Abstract Syntax Notation (ASN.1) is a formal data description language that has been developed by the computer industry
C.	All the information found in other forms of sequence storage, e.g., the GenBank format, is present. For example, sequences can be retrieved in this format by ENTREZ
D.	Taxonomic information and bibliographic information cannot be encoded with this format
Answer» E.

118.	Which of the following is wrong about National Biomedical Research Foundation/Protein Information Resource Sequence Format?
A.	Sequences retrieved from the PIR database are not in this compact format, but in an expanded format with much more information about the sequence
B.	The NBRF format is similar to the FASTA sequence format but with significant differences
C.	This is different than PIR format
D.	The first line includes an initial “>” character followed by a two-letter code such as P for complete sequence or F for fragment, followed by a 1 or 2 to indicate type of sequence, then a semicolon, then a four- to six-character unique name for the entry
Answer» D. The first line includes an initial “>” character followed by a two-letter code such as P for complete sequence or F for fragment, followed by a 1 or 2 to indicate type of sequence, then a semicolon, then a four- to six-character unique name for the entry

119.	In Stanford University/Intelligenetics Sequence Format At the end of the sequence, a 1 is placed if the sequence is linear, and a 2 if the sequence is circular.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

120.	Which of the following is wrong about Genetics Computer Group Sequence Format?
A.	Earlier versions of the Genetics Computer Group (GCG) programs require a unique sequence format and include programs that convert other sequence formats into GCG format
B.	Information about the sequence in the GenBank entry is not included but the line information is carried out
C.	If one or more sequence characters become changed through error, a program reading the sequence will be able to determine that the change has occurred because the checksum value in the sequence entry will no longer be correct
D.	Lines of information are terminated by two periods, which mark the end of information and the start of the sequence on the next line
Answer» C. If one or more sequence characters become changed through error, a program reading the sequence will be able to determine that the change has occurred because the checksum value in the sequence entry will no longer be correct

121.	In Organization of the GenBank database and the search procedure used by ENTREZ—each row is another sequence entry and each column another GenBank field.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

122.	The format of an entry in the SwissProt protein sequence database is very similar to the EMBL format.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Explore topic-wise MCQs in Bioinformatics.

Granting agency requires a certain level of accuracy in case of errors. Which of the given statements is untrue regarding it?

NCBI reviews new entries and updates existing ones, as requested.

Once the correct map has been obtained, unique overlapping clones are chosen for sequencing.

An alternative method is to sequence all the subclones, produce a computer database of the sequences, and then have the computer assemble the sequences from the overlaps that are found.

Which of the following is untrue about Shotgun Sequencing?

Which of the given statements is incorrect about READSEQ?

BL contains information about the block: xxx is the amino acids in the spaced triplet found by MOTIF upon which the block is based.

Which of the given statements is incorrect about Block multiple sequence alignment format?

Data files that have multiple sequences, such as those required for multiple sequence alignment and phylogenetic analysis using parsimony (PAUP), are not converted in READSEQ.

The “from” programs convert sequence files from GCG format into the named format, and the “to” programs convert the alternative format into GCG format.

Which of the given statements is untrue?

According to standard amino acid code letters which of the given pair is not right?

For computer analysis of proteins, it is more convenient to use single-letter than three letter amino acid codes.

Which of the given statements is incorrect?

Which of the given statements is incorrect about ASCII and Hexadecimal?

Which of the following is wrong about FASTA Sequence Format?

Which of the following is wrong about Abstract Syntax Notation Sequence Format?

Which of the following is wrong about National Biomedical Research Foundation/Protein Information Resource Sequence Format?

In Stanford University/Intelligenetics Sequence Format At the end of the sequence, a 1 is placed if the sequence is linear, and a 2 if the sequence is circular.

Which of the following is wrong about Genetics Computer Group Sequence Format?

In Organization of the GenBank database and the search procedure used by ENTREZ—each row is another sequence entry and each column another GenBank field.

The format of an entry in the SwissProt protein sequence database is very similar to the EMBL format.

Which of the following is wrong about European Molecular Biology Laboratory Data Library Format?

Which of the following is wrong about GenBank DNA Sequence Entry?

A consecutive set of three-letter words that could be codons specifying the amino acid sequence of a protein. The sequence entry is assumed by computer programs to lie between the identifiers “ORIGIN” and “//”.

The ultimate step in genome analysis is to collect the information found on gene and protein sequences, alignments, gene function and location, protein families and domains, relationships of genes to those in other organisms, chromosomal rearrangements, and so on, into a comprehensive database.

In addition to the care needed in organizing genome databases, a great deal of human input is needed to annotate the genome manually with information.

In Reverse-genetics analysis of gene function– Even though a particular gene may be _____ ortholog of a gene of known function in another organism, that gene may be acquired by a _____ function.

A genome database may also be interfaced with other types of data, such as clinical data.

To assist in finding suitable terms, for each field, ENTREZ provides a list of index entries.

For a protein search, which of the following is the wrong choice for fields?

The databases Genbank, EMBL and DDBJ are updated daily.

Using boolean logic, the search looks for database entries that include the first term __________ the second, and subsequent terms repeated until the last term.

Which of the following is incorrect about ENTREZ?

Once a set of genes that are co-regulated has been found, the promoter regions of these genes may be analyzed for conserved patterns that represent sites of interaction with specific transcription factors.

Which of the given statements is incorrect about global gene regulation?

Comparative genomics includes a comparison of gene number, gene content, and gene location in both prokaryotic and eukaryotic groups of organisms.

An approach to classification of genes that encode enzymes is to examine relationships among multiple enzymes that perform the same biochemical function in the same organism.

Processed pseudogenes are also derived from a functional gene and they contain introns and a promoter.

Which of the given statement is incorrect about proteome analyses?

The first bacterial genome to be sequenced was that of ________ a mild human pathogen.

SVMs (Support vector machines) are a binary classification method to discriminate one set of data points from another.

Telomeres hold newly replicated daughter chromosomes together.

Which of the given statements is incorrect about Family and Domain Analysis?

More than _____ of the human genome consists of interspersed repetitive sequences derived from TEs (transposable elements).

AN_ALTERNATIVE_METHOD_IS_TO_SEQUENCE_ALL_THE_SUBCLONES,_PRODUCE_A_COMPUTER_DATABASE_OF_THE_SEQUENCES,_AND_THEN_HAVE_THE_COMPUTER_ASSEMBLE_THE_SEQUENCES_FROM_THE_OVERLAPS_THAT_ARE_FOUND.?$

Which_of_the_following_is_untrue_about_Shotgun_Sequencing?$

Once the correct map has been obtained, unique overlapping clones are chosen for sequencing?

Many levels of clone redundancy may be required to build a consensus map because individual clones can have _______

In Reverse-genetics analysis of gene function– Even though a particular gene may be _ ortholog of a gene of known function in another organism, that gene may be acquired by a _ function.

123.	Which of the following is wrong about European Molecular Biology Laboratory Data Library Format?
A.	EMBL maintains DNA and protein sequence databases
B.	As with GenBank entries, a large amount of information describing each sequence entry is given
C.	Sequence entry includes literature references and information about the function of the sequence, but not locations of mRNAs and coding regions
D.	Information is organized into fields, each with an identifier, shown as the first text on each line
Answer» D. Information is organized into fields, each with an identifier, shown as the first text on each line

124.	Which of the following is wrong about GenBank DNA Sequence Entry?
A.	The information is organized into fields, each with an identifier, shown as the first text on each line
B.	In some entries, these identifiers may be abbreviated to two letters, e.g., RF for reference
C.	Some identifiers may have additional subfields
D.	The CDS subfield in the field FEATURES does not offer the amino acid sequence
Answer» E.

125.	A consecutive set of three-letter words that could be codons specifying the amino acid sequence of a protein. The sequence entry is assumed by computer programs to lie between the identifiers “ORIGIN” and “//”.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

126.	The ultimate step in genome analysis is to collect the information found on gene and protein sequences, alignments, gene function and location, protein families and domains, relationships of genes to those in other organisms, chromosomal rearrangements, and so on, into a comprehensive database.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

127.	In addition to the care needed in organizing genome databases, a great deal of human input is needed to annotate the genome manually with information.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

129.	In case of functional genomics– Two general types of approaches are used—one in which a genetic construct is made that interferes with the expression of a particular gene (and sometimes a set of related genes) and a second in which a large number of random mutations are generated in a population of organisms.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

130.	A genome database may also be interfaced with other types of data, such as clinical data.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

131.	To assist in finding suitable terms, for each field, ENTREZ provides a list of index entries.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

132.	For a protein search, which of the following is the wrong choice for fields?
A.	Accession (number)
B.	E. C. number
C.	Issue
D.	Journal number
Answer» E.

133.	The databases Genbank, EMBL and DDBJ are updated daily.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False