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Right OPTION is (d) In no case the two duplicated genes both undergo change

To explain I would say: In a possibility, two duplicated genes both undergo change, but interactions between the PROTEINS stabilize the original function and support the evolution of new ones. Through MUTATION and natural selection, one of the copies can develop a new function, LEAVING the other copy to cover for the original function. However, because most mutations are deleterious to function, often one of the copies becomes a PSEUDOGENE. Not all gene duplications are thought to have the above effects.

The correct choice is (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

To explain I would SAY: The file transfer program (FTP) has ASCII and binary modes, which may be set by the user. Some communications software can be set to ignore such control character. The use of windows on a computer has simplified such problems, SINCE one merely has to copy a sequence from one window, for example, a window that is RUNNING a Web browser on the ENTREZ Web site, and paste it into another, for example, that of a translation program.

Correct CHOICE is (a) True

To ELABORATE: There has been a great deal of progress in developing COMPUTATIONAL methods for analyzing genomic SEQUENCES and finding these protein-encoding regions. But these methods are not COMPLETELY reliable and, furthermore, such genomic sequences are often not available.

The correct choice is (a) separate, size

To explain I would say: A computer program then determines the PROBABLE order of the bands and predicts the sequence. Depending on the ACTUAL procedure being used, one RUN may generate a RELIABLE sequence of as many as 500 nucleotides.

The correct answer is (a) True

Explanation: Human and MOUSE chromosomal REGIONS that have a low density of GENES are AT-rich and have more Alu or B1/B2 (SINES) than LINE1 elements. WHEREAS the reverse is true for regions that have a high gene density, and those regions are more GC-rich.

Right choice is (d) 25 bp, 4 bp

The best I can explain: They are also FOUND in EUKARYOTIC Genomes. MICROSATELLITE repeats are found at the ends of eukaryotic chromosomes at the telomeres, which in humans comprise hundreds of copies of a 6-bp repeat TTAGGG.

Right option is (a) There is no simple way to find the CORRECT sequence without manually checking the information provided in each sequence, but this usually takes LONGER time

To explain: Opposite to what is mentioned in option a, this takes shorter time. It is important to look through the SEQUENCES to locate the one intended. There may be several different copies of the sequence because it may have been SEQUENCED from more than one organism, or the sequence may be a mutant sequence, a particular clone, or a fragment.

Correct choice is (b) accession number, protein name, or name of gene

To elaborate: If the same protein has been sequenced in several ORGANISMS, PROVIDING an organism name is also helpful. When the chosen SEARCH terms and fields have been decided and submitted, a database comprising all of the currently available SEQUENCES (called the non redundant or NR database) will be SEARCHED. Other database selections can also be made.

Right option is (a) True

For explanation: Data FILES with such multiple sequences as mentioned are converted in READSEQ. OPTIONS to reverse-complement and to remove gaps from sequences are included. SEQIO and another SEQUENCE conversion program for a UNIX machine.

Right choice is (C) This is different than PIR format

Easy explanation: This sequence format, which is sometimes also called the PIR format. It has been used by the NATIONAL BIOMEDICAL Research Foundation/Protein Information Resource (NBRF) and also by other sequence analysis programs.

Correct answer is (b) When DNA fragments derived from different chromosomal regions have repeats of the same sequence, they will appear to scrutinize

The explanation: A controversy has arisen as to whether or not the above shotgun sequencing strategy can be applied to genomes with repetitive sequences such as those likely to be encountered in sequencing the human genome. This method has been used to assemble the genome of the fruit fly Drosophila melanogaster after REMOVAL of the most HIGHLY repetitive regions and also to assemble a SIGNIFICANT proportion of the human genome.

Correct option is (c) The transferred materialbecomes a TEMPORARY addition to the recipient genome

Best EXPLANATION: The transferred material BECOMES a permanent addition to the recipient genome. Although these EXCHANGES do not occur very often on a generation-to-generation basis, a significant number can occur over a period of hundreds of MILLIONS of years.

Correct choice is (c) The conservative approach is to group distinct sequences

To explain I would say: The conservative approach is to group only very SIMILAR sequences together. However, in making a conservative MULTIPLE sequence alignment with only very alike sequences, it is not POSSIBLE to analyze the evolutionary divergence that may have occurred in a family of proteins. Furthermore, if a matrix or profile MODEL is MADE from this alignment, that model will not be useful for identifying more divergent members of a family.

The correct ANSWER is (b) An abnormal properties of the mutant organism does not REVEAL the gene function

Easy explanation: The gene function is revealed by any abnormal properties of the mutant organism. This methodology provides a way to test a gene function that is predicted by sequence similarity to be the same as that of a gene of known function in another organism. If the other organism is very different biologically (comparing a predicted plant or animal gene to a known yeast gene), then FUNCTIONAL genomics can also SHED light on any newly ACQUIRED biological role.

Correct OPTION is (a) True

For explanation I would say: It is started by a MOLECULAR genetics group at Stanford University, and subsequently continued by a company, Intelligenetics, the IG format is SIMILAR to the PIR format, except that a semicolon is usually placed before the comment line. The identifier on the second line is ALSO present.

Right CHOICE is (c) A match of a predicted PROTEIN SEQUENCE to one or more database sequencesserves only to identify the gene function but it doesn’t validate the gene prediction

Easiest EXPLANATION: A match of a predicted protein sequence to one or more database sequences not only serves to identify the gene function, but also validates the gene prediction. Pseudogenes, gene copies that have lost function, may also be found in this analysis.

Correct choice is (b) False

Explanation: Processed pseudogenes are ALSO derived from a functional gene, but they do not contain introns and LACK a promoter; hence, they are not expressed. The origin of these pseudogenes is probably DUE to reverse TRANSCRIPTION of the mRNA of the functional gene and INSERTION of the cDNA copy into a new chromosomal location by a LINE1 reverse transcriptase.

The correct choice is (b) False

To explain I WOULD say: TEs (Transposable Elements) can comprise one-half or more of the genome sequence. Eukaryotic genomes comprise CLASSES of REPEATED elements, including tandem repeats present in centromeres and TELOMERES, dispersed tandem repeats (MINISATELLITES and macrosatellites), and interdispersed TEs.

The correct CHOICE is (C) Chromosomes of a TARGET organism are purified, fragmented, and subcloned in fragments of size hundreds of bp

Easy explanation: Chromosomes of a target organism are purified, fragmented, and subcloned in fragments of size hundreds of KBP and not bp.The BAC fragments are then further subcloned as smaller fragments into plasmid vectors for DNA sequencing.

Correct option is (c) 80–300 BP long

To elaborate: There exists also (6–8 kbp long) interspersed NUCLEAR elements (LINES). Different types of TRANSPOSABLE elements are present in high COPY numbers in mammalian genomes in varying manner.

The correct option is (a) True

The explanation is: The THREE branches are represented by Archaea, the Bacteria, and the Eukarya. Analysis of the ribosomal for GENOME sequencing projects, organisms have been sampled from throughout the tree, including some that are in DEEPER branches of the tree and that have growth properties reminiscent of an ancient environment.

Right answer is (b) Other projects may BENEFIT from the availability of better CURATED and annotated protein sequence databases, but not PIR and SwissProt

For explanation: Curated and annotated protein sequence databases include PIR and SwissProt. When read from cDNA copies of MRNA SEQUENCES, they provide a reliable sequence, given a certain amount of uncertainty as to the translational start site. Many protein sequences are now predicted by translation of genomic sequences, requiring a prediction of exons, a SOMEWHAT error-prone step.

Correct answer is (a) True

To EXPLAIN I would say: NCBI STANDS for National CENTER for Biotechnology Information. It MANAGES GenBank. DDBJ and EMBL stand for DNA Database Bank of Japan and European Molecular BIOLOGY Laboratory respectively.

Correct option is (a) True

Easy explanation: Genomic sequencing MEETS both GOALS. However, only a small percentage of the genomic sequence of many organisms actually ENCODES proteins because of the presence of introns WITHIN coding regions and other NONCODING regions in the genome.

Right choice is (b) 100-kb

The explanation: To sequence LARGER molecules, such as HUMAN chromosomes, individual chromosomes are purified and BROKEN into 100-kb or larger random fragments, which are cloned into vectors designed for large molecules, such as artificial yeast (YAC) or bacterial (BAC) chromosomes. In a laborious procedure, the resulting library is screened for fragments called contigs, which have overlapping or common sequences, to PRODUCE an integrated map of the CHROMOSOME.

Correct CHOICE is (a) True

Best explanation: By repeating this procedure, both strands of a DNA fragment several kilobases in LENGTH can be sequenced. SEQUENTIAL sequencing of a DNA molecule USING oligonucleotide primers is done LATER.

Correct answer is (c) The number of protein sequences that are AVAILABLE is insufficient to determine that domain shuffling OCCURS in evolution

Easiest explanation: The number of protein sequences is sufficient unlike mentioned in option c. The comparisons of PROTEOMES of different organisms can identify the type of domain CHANGES and also provide an indication as to what biological ROLE they may have in a particular organism.

Correct answer is (d) Gene locations

Easiest EXPLANATION: Map locations of orthologous genes may also be compared. If a set of genes is GROUPED together at a particular chromosomal location, and if a set of similar genes is also grouped together in the genome of another organism, these GROUPS share an EVOLUTIONARY history.

Correct choice is (d) Each protein of ONE PROTEOME is selected in TURN as a query of the proteome of another single organism only

Easiest explanation: This analysis can predict orthologs. In other words proteins have an IDENTICAL function attributable to descent of the RESPECTIVE genes from a common ancestor.

The correct answer is (a) True

To explain I WOULD say: EUKARYOTIC genomes commonly have tandem repeats of SEQUENCES. In addition to this, they having LINEAR chromosomes within a nucleus, and DIFFERING from prokaryotic genomes in this respect.

Right choice is (a) True

To EXPLAIN I would say: When SEARCHING for terms in a particular field, some knowledge of the terms that are in the database can be helpful. The “Limits” LINK on the ENTREZ form page is used to limit the GenBank field to be searched, and various logical COMBINATIONS of search terms may be designed by this method. These FIELDS refer to the GenBank fields.

Correct OPTION is (b) The identifier is terminated by a COMMA, and “BLOCK” indicates the entry type

The best explanation: The identifier is terminated by a semicolon, and “BLOCK” indicates the entry type. Min, max is the minimum, maximum number of AMINO acids from the previous blocks or from the sequence STARTING. DE describes sequences from which the block was made.

Correct choice is (a) SEARCHES of EST databases for matches to a query SEQUENCE routinely produce minimal amounts of output that must be searched manually for significant hits

The explanation: The Searches of EST databases for matches to a query sequence routinely produce large amounts of output that must be searched manually for significant hits.an automatic method was DESCRIBED in 1999 utilizing a COMPUTER script, FAST-PAN, that scans EST databases with multiple queries from a protein family, sorts the alignment scores, and produces CHARTS and alignments of the matches found.

Correct answer is (a) 400 bp

The best I can explain: They were DISCOVERED in diverse flowering PLANTS where they are frequently associated with regulatory regions of genes. HENCE, they COULD be exerting an influence on REGULATION of gene expression.

Correct option is (a) True

Easy explanation: The COST and efficiency of this process has been greatly improved by AUTOMATIC methods of sequence assembly, first used for the sequencing of the BACTERIUM H. influenza. This same method of assembly was also used, in part, to complete the sequencing of the Drosophila and human genomes in a timely manner.

The CORRECT answer is (a) True

The EXPLANATION is: Other features of eukaryotic genes in a particular organism that are useful for gene prediction include the consensus sequences at exon–intron and intron–exon splice junctions, base composition, codon usage, and preference for neighboring codons. Computational methods incorporate this INFORMATION into a gene model that MAY be used to predict the PRESENCE of genes in a genome sequence.

Right option is (B) 1.8 x 10^6 bp

Explanation: It was done excepting SEVERAL regions that had to be assembled manually. Once AVAILABLE, open reading frames were identified, and these were compared to the EXISTING proteins by a database similarity search.

Correct answer is (d) reference number type(s)

EASIEST explanation: In addition to these KEYWORDS that apply to sequence, features in the sequence such as CODING regions, intron splice sites, and mutations; and finally the sequence itself is given the sequence database ENTRY. The above information is organized into a tabular FORM very much like that found in a relational database.

Right choice is (a) RELATIONAL databases are more USEFUL in the development of biological databases

To explain: The OBJECT-oriented database structure has been useful in the development of biological databases. The objects, such as GENETIC MAPS, genes, or proteins, each have an associated set of utilities for analysis and display of the object and a set of attributes such as identifying name or references.

Correct choice is (d) TAXONOMIC information and bibliographic information cannot be encoded with this format

For explanation I would say: ASN.1 has been adopted by the NATIONAL Center for BIOTECHNOLOGY Information (NCBI) to encode data such as sequences, maps, taxonomic information, molecular structures, and bibliographic information. These data sets may then be EASILY connected and accessed by computers. The ASN.1 sequence format is a highly structured and detailed format especially designed for COMPUTER access to the data.

Right option is (a) True

To EXPLAIN I would say: When one sequence entry is RETRIEVED, all of these fields will be DISPLAYED. Search for the term “SOS regulon and coli” in all fields will find two MATCHING sequences. FINDING these sequences is simple because indexes have been made listing all of the sequences that have any given term, one index for each field. Similarly, a search for transcriptional regulator will find three sequences.

Right option is (a) True

To elaborate: For example, GenBank DNA sequence entries contain a TRANSLATED sequence in single-letter code. The STANDARD, single-letter AMINO acid code was established by a joint international committee.