130 + Interview Questions in Collecting & Storing Sequences In Laboratory in Bioinformatics Page 3 InterviewSolution

101.	Using ddATP, the resulting synthesis creates a set of nested DNA fragments, each one ending at one of the as in the sequence through the substitution of a fluorescent-labeled ddATP.(a) True(b) FalseI have been asked this question during an online exam.The origin of the question is DNA & Genomic Sequencing topic in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The CORRECT option is (a) True The explanation is: A SIMILAR set of FRAGMENTS is made for each of the other three bases. But each set is LABELED with a different fluorescent ddNTP.

Discussion

102.	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- serineThe question was posed to me during an interview.The query is from Sequence Formats & Computer Storage of Sequences in division Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Correct answer is (d) R- serine The EXPLANATION: In ADDITION to the standard four base symbols, A, T, G, and C, the Nomenclature Committee of the International Union of Biochemistry has established a standard code to represent bases in a nucleic ACID sequence that is uncertain or ambiguous. R is represented by ARGININE.

Discussion

103.	In the program COGNITOR each protein in the proteome is used as a query of a database of protein clusters.(a) True(b) FalseI had been asked this question in homework.My question is taken from Sequence Assembly and Gene Identification in division Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Correct answer is (a) True Easiest explanation: The database was made by PERFORMING an all-by-all genome COMPARISON across a spectrum of prokaryotic organisms and a portion of the YEAST proteome. Orthologous pairs of sequence were then merged with clusters or orthologous pairs (COGs) for MULTIPLE proteomes.

Discussion

104.	The sequences of satellite DNA fall into different types, each with a different repeat unit of length _____(a) 5–400 Mbp(b) 3–300 kbp(c) 6–900 Mbp(d) 5–200 bpI had been asked this question in examination.Asked question is from Genome Anatomy in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Right choice is (d) 5–200 bp To explain I would say: Because of the skewed base composition of regions that have repeats, they MAY be PURIFIED by virtue of having different buoyant densities. The repeat unit of length is 5–200 bp and not in the SCALE if MEGA.

Discussion

105.	Which of the given features is incorrect?(a) TEs are present in few particular chromosomes(b) TEs are present in all of the chromosomes(c) Abundance of TEs varies(d) TEs can comprise a large portion of the genomes of higher eukaryotes, both plants and animalsThe question was posed to me during an interview for a job.This interesting question is from Genome Anatomy in section Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Correct option is (a) TEs are present in few particular chromosomes For explanation I would say: TEs are present in all of the chromosomes, ranging from bacteria to humans, but their abundance varies. They can comprise a large portion of the genomes of higher eukaryotes, THUS, only a small fraction of the genome of these ORGANISMS CARRIES GENE sequences.

Discussion

106.	In examining the results of analysis, it is important to look for the method used the statistical significance of the result, and the overall degree of confidence in the alignments.(a) True(b) FalseI got this question during an interview.This key question is from Genome Anatomy in portion Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Right ANSWER is (a) True Explanation: The ANALYSIS should be repeated if necessary. Annotation errors OCCUR when the above criteria are not followed.

Discussion

107.	While sequencing of The first bacterial genome—Approximately ____ of the ____predicted genes matched genes of another species, the bacterial species E. coli K-12 that had been the subject of many years of genetic and biochemical research.(a) 46%, 1500(b) 58%, 1496(c) 72%, 1743(d) 58%, 1743The question was posed to me during a job interview.The above asked question is from Genome Anatomy topic in section Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» RIGHT option is (d) 58%, 1743 The best explanation: The function of the other 42% of the Hemophilus genes could not be identified, although some of them were similar to the 38% of E. coli genes that were also of UNKNOWN function. Other UNIQUE SEQUENCES that appeared to be associated with the ability of the organism to behave as a human pathogen were also found.

Discussion

108.	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 charactersI have been asked this question by my school teacher while I was bunking the class.I'd like to ask this question from Sequence Formats & Computer Storage of Sequences topic in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer»

Discussion

109.	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) FalseThe question was posed to me in class test.The above asked question is from Sequence Formats & Computer Storage of Sequences in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The correct answer is (a) True Easy explanation: The SEQUENCE includes numbers on each LINE so that sequence positions can be located by eye. Because the sequence count or a sequence checksum value may be used by the computer program to verify the sequence COMPOSITION, the sequence count should not be modified EXCEPT by programs that ALSO modify the count. The GenBank sequence format often has to be changed for use with sequence analysis software.

Discussion

110.	Which of the following is untrue about DNA sequencing methods?(a) Purified fragments of DNA cut from plasmid/phage clones or amplified by polymerase chain reaction (PCR)(b) Clones of DNA fragments are denatured to single strands, and one of the strands is hybridized to an oligonucleotide primer(c) Taq polymerase is quite heat sensitive(d) New strands of DNA are synthesized from the end of the primerI had been asked this question during an interview.My enquiry is from DNA & Genomic Sequencing topic in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The correct answer is (C) TAQ polymerase is quite heat sensitive The best explanation: In an automated procedure, new strands of DNA are synthesized from the end of the primer by heat-resistant Taq polymerase from a POOL of deoxyribonucleotide triphosphates (dNTPs) that includes a small amount of one of four chain-terminating NUCLEOTIDES (ddNTPs).

Discussion

111.	Which of the given statements is incorrect about All-against-all Self-comparison?(a) A comparison of each protein in the proteome with all other proteins distinguishes unique proteins from proteins that have arisen from gene duplication, and also reveals the number of protein families but the domain content of these proteins cannot be known(b) In all-against-all proteome comparison, each protein is used as a query in a similarity search against the remaining proteome(c) In all-against-all proteome comparison, the similar sequences are ranked by the quality and length of the alignments found(d) In all-against-all proteome comparison, The search is conducted with each alignment score receiving a statistical evaluation (P or E value)This question was posed to me during an online interview.This is a very interesting question from Comparative Genomics topic in section Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The correct answer is (a) A comparison of each protein in the proteome with all other proteins distinguishes unique proteins from proteins that have arisen from GENE duplication, and also reveals the NUMBER of protein families but the DOMAIN CONTENT of these proteins cannot be known For explanation I would say: The domain content of these proteins may also be analyzed. in all-against-all proteome comparison, a match between a query sequence and another proteome sequence with the same domain structure will produce a high-scoring, highly significant ALIGNMENT. These proteins are designated paralogs because they have almost certainly originated from a gene duplication event.

Discussion

112.	In all-against-all self comparison, A comparison is made in which every protein is used as a query in a similarity search against a database composed of the rest of the proteome, and the significant matches are identified by a low expect value.(a) True(b) FalseThe question was posed to me during a job interview.This is a very interesting question from Sequence Assembly and Gene Identification topic in division Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The correct CHOICE is (a) True The best I can explain: Many proteins comprise different combinations of a common SET of domains, proteins that align along most of their lengths (80% identity is a CONSERVATIVE choice). Hence they are chosen to select those that have a conserved domain structure.

Discussion

113.	Which of the given statement is incorrect about the gene map?(a) Gene order in two related organisms reflects the order that was present in a common ancestor genome. Chromosomal breaks followed by reassembly of fragments in a different order can produce new gene maps(b) Gene order is only revealed by the physical order of genes on the chromosome(c) Sequence variations (polymorphisms) that are close to (tightly linked) a trait may be used to trace the trait by virtue of the fact that the polymorphism and the trait are seldom separated from one generation to the next(d) These types of evolutionary changes in genomes have been modeled by computational methodsThe question was posed to me during an interview.I need to ask this question from Sequence Assembly and Gene Identification topic in section Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Correct answer is (B) Gene order is only revealed by the physical order of genes on the chromosome Explanation: Gene order is revealed not only by the physical order of genes on the chromosome but also by genetic analysis. Populations of an organism show sequence variations that are readily detected by DNA SEQUENCING and other analysis methods. The inheritance of genetic diseases in humans and ANIMALS (e.g., cancer and heart disease), and of desirable traits in plants, can be traced genetically by PEDIGREE analysis or genetic crosses.

Discussion

114.	______ can comprise a large proportion of the eukaryotic genome as ______(a) transposable elements, single copy sequences(b) transposable elements, repetitive sequences(c) macrosatellite DNA elements, single copy sequences(d) satellite DNA elements, single copy sequencesThis question was addressed to me in an online interview.My query is from Genome Anatomy in division Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The correct answer is (b) TRANSPOSABLE ELEMENTS, repetitive sequences The best explanation: Transposable elements (TEs) are thought to play an important role in the evolution of these genomes. TEs are DNA sequences that can MOVE from one chromosomal location to another faster than the chromosome can replicate.

Discussion

115.	In nondividing cells, a mixture of lightly and darkly stained chromosomal regions called euchromatin and heterochromatin respectively, are observed.(a) True(b) FalseThis question was posed to me in an interview for job.The doubt is from Genome Anatomy in division Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Correct CHOICE is (b) False Easiest explanation: In nondividing CELLS, a mixture of lightly and darkly STAINED chromosomal regions called heterochromatin and euchromatin RESPECTIVELY, are observed. The centromeric and telomeric regions are located in the heterochromatin, which is in a compact configuration and is thought not to be transcribed.

Discussion

116.	The Common Object Request Broker Architecture (CORBA) is the Object Management Group’s interface for objects.(a) True(b) FalseThis question was posed to me during an online interview.My question is from Multiple Sequence Formats & Storage of Information in a Sequence Database topic in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» CORRECT option is (a) True Easy explanation: It ALLOWS different computer applications to communicate with each other through a COMMON language, Interface Definition Language (IDL). To PLAN an object-oriented database by defining the classes of objects and the relationships among these objects, a specific SET of procedures called the Unified Modeling Language (UML) has been devised by the OMG group.

Discussion

117.	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) FalseThe question was posed to me in an international level competition.The doubt is from Multiple Sequence Formats & Storage of Information in a Sequence Database topic in section Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Right answer is (a) True The best I can EXPLAIN: In ADDITION, the GCG PROGRAMS include the FOLLOWING sequence formatting programs: (1) GETSEQ, which converts a simple ASCII file being received from a remote PC to GCG format; (2) REFORMAT, which will format a GCG file that has been edited, and will also perform other functions; and (3) SPEW, which sends a GCG sequence file as an ASCII file to a remote PC.

Discussion

118.	Which of the given statement is incorrect about Clusters of functionally related genes?(a) In microbial genomes, genes specifying a metabolic pathway may be contiguous on the genome where they are coregulated transcriptionally in an operon by a common promoter(b) In related organisms, gene order on the chromosome is least likely to be conserved(c) As the relationship between the organisms decreases, local groups of genes remain clustered together, but chromosomal rearrangements move the clusters to other locations(d) The function of a particular gene can sometimes be predicted, given the known function of a neighboring, closely linked geneThis question was addressed to me in unit test.My question is based upon Sequence Assembly and Gene Identification in portion Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The correct CHOICE is (b) In related organisms, gene ORDER on the chromosome is least LIKELY to be conserved Easiest explanation: In related organisms, both gene CONTENT of the genome and gene order on the chromosome are likely to be conserved.

Discussion

119.	Which of the given statements is incorrect about Family and Domain Analysis?(a) Gene identification of predicted proteins in the genome is designed to discover the metabolic features of an organism(b) In a particular organism or group of organisms, one particular domain can be expanded to perform a particular function(c) 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(d) Different proteins are mosaics of domains that occur in different combinations in a given proteinThis question was addressed to me at a job interview.Origin of the question is Comparative Genomics topic in portion Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Right choice is (b) In a PARTICULAR ORGANISM or GROUP of organisms, one particular domain can be expanded to perform a particular function Easiest explanation: In a particular organism or group of organisms, various DOMAINS can be expanded to perform a particular function. More than 2000 fly and worm PROTEINS are multidomain proteins, compared to about one-third this number in yeast.

Discussion

120.	An all-against-all analysis requires first making a database of the proteome. This database is then sequentially searched by each individual protein sequence of the proteome using a rapid database similarity search tool such as _______(a) XPBLAST(b) WU-BLAST(c) BLAST(d) FASTAThis question was posed to me during an interview.My doubt stems from Sequence Assembly and Gene Identification in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Right choice is (a) XPBLAST The EXPLANATION: P values of WU-BLAST are similar to E values of NCBI BLAST (Rubin et al. 2000) for values of P and E < 0.05. This analysis generates a matrix of alignment scores, each with an E value and CORRESPONDING alignment for each pair of proteins. Also, the E value of an alignment score is the probability that an alignment score as good as the ONE found WOULD be observed between two random or unrelated sequences in a search of a database of the same size.

Discussion

121.	Genes that are transcribed are located in the ______(a) euchromatin(b) heterochromatin(c) heterochromatin and euchromatin(d) tightly bound DNAI had been asked this question in homework.Query is from Genome Anatomy in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The correct choice is (a) EUCHROMATIN Explanation: They are located in the LESS compact euchromatin. This GIVES the REGULATORY proteins access to the genetic material.

Discussion

122.	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 lineI got this question during an interview for a job.Enquiry is from Sequence Formats & Computer Storage of Sequences topic in section Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Right choice is (c) Sequence entry includes LITERATURE references and information about the function of the sequence, but not LOCATIONS of mRNAs and coding regions Explanation: Sequence entry includes literature references and information about the function of the sequence, locations of mRNAs and coding regions and positions of important mutations. The sequence COUNT or a CHECKSUM value for the sequence may be used by computer programs to make sure that the sequence is complete and accurate. For this reason, the sequence part of the entry should usually not be modified except with programs that also modify this count.

Discussion

123.	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 sequenceI got this question in a job interview.I'd like to ask this question from Sequence Formats & Computer Storage of Sequences in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The correct choice is (d) The CDS subfield in the field FEATURES does not offer the amino ACID sequence Best explanation: The CDS subfield in the field FEATURES gives the amino acid sequence obtained by translation of known and potential open reading frames. The format of a database entry in GenBank, the NCBI nucleic acid and protein sequence database, is as follows: Information describing each sequence entry is given, INCLUDING literature references, information about the function of the sequence, LOCATIONS of mRNAs and coding regions, and positions of important mutations.

Discussion

124.	The all-against-all analyses provide an indication as to the number of protein/gene families in an organism. This number represents the core proteome of the organism from which all biological functions have diversified.(a) True(b) FalseThis question was posed to me in an interview for internship.Question is from Comparative Genomics topic in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Correct option is (a) True Best EXPLANATION: In Hemophilus, 1247 of the total NUMBER of 1709 proteins do not have paralogs. The CORE proteomes of the worm and fly are similar in size but with a greater number of duplicated genes in the worm. It is QUITE remarkable that the core PROTEOME of the multicellular organisms (worm and fly) is only twice that of yeast.

Discussion

125.	Which of the given statements is incorrect about Clustering by making subgraphs?(a) Each sequence is a vertex and each pair of sequences that is matched with a significant alignment score is joined by an edge that is weighted according to the statistical significance of the alignment score(b) One way to identify the most strongly supported clusters is simply to add the most weakly supported edges in the graph(c) One way to identify the most strongly supported clusters is simply to remove the most weakly supported edges in the graph(d) An edge is weighted according to the statistical significance of the alignment scoreThe question was posed to me in my homework.The above asked question is from Comparative Genomics topic in division Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Right choice is (c) One way to IDENTIFY the most strongly supported clusters is simply to remove the most weakly supported edges in the graph The explanation is: As weaker and weaker links are removed, the remaining combinations of vertices and edges represent most strongly linked sequences. This type of ANALYSIS was performed on an initial collection of E. coli genes by Labedan and Riley (1995).

Discussion

126.	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) FalseI have been asked this question during an online interview.I would like to ask this question from Multiple Sequence Formats & Storage of Information in a Sequence Database topic in division Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Right option is (a) True For EXPLANATION: In addition to this, w is the width of the sequence segments (columns) in the BLOCK. s is the number of sequence segments (rows) in the block. Other values (n1, N2) describe statistical features of the block. Sequence ID is a list of SEQUENCES. Each sequence line contains a sequence identifier, the offset from the beginning of the sequence to the block in parentheses, the sequence segment, and a weight for the segment.

Discussion

127.	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 frameshiftsI have been asked this question in an international level competition.Question is taken from Sequencing cDNA Libraries of Expressed Genes, Submission of Sequences to the Databases topic in division Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer»

Discussion

128.	NCBI reviews new entries and updates existing ones, as requested.(a) True(b) FalseI had been asked this question in quiz.I'd like to ask this question from Sequencing cDNA Libraries of Expressed Genes, Submission of Sequences to the Databases topic in section Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» The CORRECT choice is (a) True Best explanation: A database accession number, which is required to PUBLISH the sequence, is provided. New SEQUENCES are exchanged DAILY by the GenBank, EMBL, and DDBJ databases.

Discussion

129.	The sequence can also be verified by making an oligonucleotide primer complementary to the distal part of the readable sequence and using it to obtain the sequence of the complementary strand on the original DNA template.(a) True(b) FalseThis question was addressed to me in examination.Origin of the question is DNA & Genomic Sequencing in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» Correct CHOICE is (a) True Best explanation: For accurate WORK, a printout of the SCAN is USUALLY examined for abnormalities that decrease the quality of the sequence, and the sequence may then be edited manually. The first sequence can also be extended by making a second oligonucleotide matching the DISTAL end of the readable sequence and using this primer to read more of the original template.

Discussion

130.	Many levels of clone redundancy may be required to build a consensus map because individual clones can have _______(a) rearrangements(b) deletions(c) two separate fragments(d) vectorsI have been asked this question in exam.My doubt stems from DNA & Genomic Sequencing in section Collecting & Storing Sequences in Laboratory of Bioinformatics
Answer» RIGHT answer is (d) vectors The explanation: Option vectors here becomes IRRELEVANT as it has quite LESS RELEVANCY to redundancy of the clones. These do not reflect the correct map and have to be ELIMINATED.

Discussion

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Genes that are transcribed are located in the ______(a) euchromatin(b) heterochromatin(c) heterochromatin and euchromatin(d) tightly bound DNAI had been asked this question in homework.Query is from Genome Anatomy in chapter Collecting & Storing Sequences in Laboratory of Bioinformatics