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Correct answer is (d) introns removed

To EXPLAIN: The only possible DIFFICULTY is that a gene of interest MAY be developmentally expressed or regulated in such a way that the mRNA is not present. This problem has been CIRCUMVENTED by pooling mRNA preparations from tissues that express a large proportion of the genome, from a variety of tissues and developing organs or from organisms subjected to several environmental INFLUENCES.

Right answer is (a) True

Explanation: Accurate annotation of genome sequences is an important first step in genome analysis. Matches of lesser significance provide only a TENTATIVE or hypothetical prediction and should be used as a working HYPOTHESIS of FUNCTION.

Correct answer is (a) True

The BEST I can explain: Functional differentiation then occurs between the COPIES by mutation and selection. However, because most mutations are deleterious, and because only one GENE copy may be needed for function, there is a strong tendency of one copy to ACCUMULATE mutations that render the gene nonfunctional.

The CORRECT ANSWER is (b) They were MODEL EUKARYOTIC organisms

Explanation: There were model prokaryotic organisms. For E.g., E. coli and Bacillus subtilis. The success of sequencing the Hemophilus genome in a relatively short time and with a modest budget heralded the sequencing of a large number of additional prokaryotic organisms.

The correct choice is (b) False

Explanation: The lower the E value, the more SIGNIFICANT the ALIGNMENT between a PAIR of matching SEQUENCES. 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.

The correct choice is (b) introns

To explain I would say: Once the sequence patterns that are characteristic of the GENES in a particular prokaryotic organism (e.g, CODON usage, codon neighbor preference) have been FOUND, gene locations in the genome sequence can be predicted quite accurately. The presence of introns in eukaryotic genomes makes gene PREDICTION more involved because, in addition to the above FEATURES, locations of intron–exon and exon–intron splice junctions must also be predicted.

Right choice is (c) Which genes are depleted at what time

To explain: For chronological information there are other numerous techniques that can be FOLLOWED. This type of information provides an indication as to which genes share a related biological function or may act in the same biochemical pathway and may thereby give clues that will assist in gene identification.

Correct choice is (a) True

The best I can explain: The mentioned database centers are updated DAILY and exchange NEW sequences daily, so that it is only necessary to access one of them. The EMBL STANDS for European MOLECULAR Biology Laboratory and DDBJ for DNA DATABANK of Japan.

Correct choice is (b) It is quite tough making an index of the information in each of these fields so that a search QUERY can locate all the OCCURRENCES through the index

To explain: It is very easy to MAKE an index of the information in each of these fields so that a search query can locate all the occurrences through the index. Even related sequences are cross-referenced. In addition, the information in one DATABASE can be cross-referenced to that in ANOTHER database.

The correct choice is (a) True

Easiest EXPLANATION: The translated sequence can then be COMPARED in the MENTIONED way HENCE to identify the function of the cloned EST. The corresponding cDNA clone of the gene of interest can then be obtained and the gene completely SEQUENCED.

Correct option is (a) True

For explanation I WOULD say: This was an important development from resolution point of view. This has just enough DNA sequence to give a GOOD idea of the protein sequence.

The correct answer is (b) An analysis of ACRs that predate the radiation of the major animal PHYLA some 580–540 million years ago SUGGESTED that 50–60% of coding sequences are ACRs

The explanation is: The analysis of ACRs 580–540 million years ago suggested that 20–40% of coding sequences are ACRs. For example, a search with 1916 E. coli PROTEINS DETECTED 266 ACRs found in 439 sequences, roughly one-quarter of the SwissProt database.

Correct answer is (d) SwissProt

To elaborate: The domain composition of each protein is also determined by searching for matches in domain DATABASES such as Interpro. The analysis reveals how MANY domains and domain COMBINATIONS are present in the proteome, and reveals any unusual representation that might have biological significance. The number of expressed genes in each family can also be compared to the number in other ORGANISMS to DETERMINE whether or not there has been an expansion of the family in the genome.

The correct option is (a) True

Easiest explanation: The availability of COMPLETE genome sequences makes POSSIBLE a comparison of all of the PROTEINS ENCODED by one genome, the PROTEOME of that organism, with those of another. Because the genome sequence provides both the sequence and the map location of each gene, both the sequence and location can be compared.

Correct choice is (b) a LARGE EXTENT, biochemical and immunological tests

Easy explanation: Moreover, changes in levels of proteins in response to an environment signal can be monitored in much the same way as a microarray analysis is performed. Microarrays only DETECT untranslated mRNAs, whereas a two-dimensional GEL protein analysis detects translation products, THUS revealing an additional level of regulation.

Correct option is (b) LTR RETROTRANSPOSONS, related

To explain I would say: There are THREE main SUBCLASSES of these TEs—the LONG terminal repeat (LTR) retrotransposons, retroposons, and retrovirus-like elements with LTRs. Class I elements encode reverse transcriptase and use RNA mediated mechanisms of transcription.

The CORRECT choice is (c) twofold, less

The explanation: Of the REMAINING genomes, C. elegans and A. thaliana have approximately the same density of genes (one gene per 6 kb). DROSOPHILA is the LEAST DENSE in this comparison (one gene per 14 kb).

The CORRECT answer is (a) True

Easy explanation: GENOME regions that encode these sequences can then be identified and the corresponding gene located. A similar METHOD MAY be used to identify the gene that ENCODES a particular protein that has been purified and characterized in the laboratory.

The correct answer is (b) 200,000 copies

To EXPLAIN I would say: The class of TEs, class II, is MADE up of ELEMENTS that employ a DNA-based MECHANISM of transposition. Class II elements also include the Activation-Dissociation (Ac-Ds) family in maize and the P element in Drosophila.

Correct option is (d) SEQUIN does not run on UNIX

To explain I would say: The other method of SUBMISSION is to use Sequin (formerly called Authorin), which RUNS on personal computers and UNIX machines. The program provides an easy-to-use GRAPHIC interface and can manage LARGE submissions such as genomic sequence information.

Right answer is (d) When two or more proteins in the proteome share a high degree of similarity they are least likely to be paralogs

To explain I would say: When two or more proteins in the proteome share a high degree of similarity because they share the same SET of domains, they are likely to be paralogs, genes that arose by gene DUPLICATION events. Proteins that ALIGN over shorter regions share some domains, but also may not share OTHERS. Although gene duplication events could have CREATED such variation, other rearrangements may have also occurred, blurring the evolutionary history.

Right option is (a) True

To explain: The origin of introns in EUKARYOTIC genes is not understood but has been accounted for by two models. The “introns-early” VIEW proposes that introns were used to assemble the first genes from sets of ANCIENT conserved exons, whereas the “introns-late” view proposes that introns broke up previously continuous genes by inserting into them.

The correct option is (a) True

To explain: For a NEW genome, each predicted gene is translated into a PROTEIN sequence; the COLLECTION of protein sequences ENCODED by the genome is the proteome of the organism. every protein in the proteome is then used as a query sequence in a database similarity SEARCH. Matching database sequences are realigned with the query sequence to evaluate the extent and significance of the alignment.

Correct answer is (B) False

Explanation: Some of it is found NEAR the open ENDS of chromosomes- telomeres but Most of this repetitive DNA is found near the centromere. It is because they serve as a point of ATTACHMENT for pulling the chromosomes APART during cell division.

The correct option is (a) True

The explanation is: Nuclei and chromosomes were not observed in bacteria (a prokaryotic cell), but when BACTERIAL DNA was eventually detected, the molecule was usually circular and was ALSO in a compacted FORM. The FOLLOWING sections outline the structure and composition of prokaryotic and EUKARYOTIC genomes.

Correct choice is (a) AND

Easiest explanation: On the ENTREZ form, MAKE a SELECTION in the data entry window after the TERM “Search,” then ENTER search terms in the longer data entry window after “for.” The database will be searched for sequence database entries that contain all of these terms or related ONES.

The correct option is (d) Journal number

The best I can EXPLAIN: Other fields being- author name, journal name, keyword, modification date. Also, it includes organism, page number, primary ACCESSION (number), properties, protein name, publication date (of reference), seqID string, sequence length, substance name, text word, title word, volume, and sequence ID. Similar fields are SHOWN for the DNA DATABASE search.

The CORRECT option is (a) True

To EXPLAIN I would SAY: It CONTAINS just a line of sequence identifiers FOLLOWED by the sequence without numbers, is very useful for browsing and analyzing purposes. One browser window may retrieve sequences from a database and a second may analyze these sequences.

The correct choice is (d) It can RECOGNIZE a DNA or protein sequence file in some particular formats

The explanation: It can identify the FORMAT, and WRITE a NEW file with an alternative format. Some of these formats are used for special types of analyses such as multiple sequence alignment and phylogenetic analysis.

The correct answer is (b) False

The best explanation: PSEUDOGENES are DNA sequences that were derived from a FUNCTIONAL copy of a gene but which have acquired mutations that are deleterious to FUNCTION. For e.g. the PSEUDOGENE TRY5 is similar to the NEARBY functional gene TRY4.

The correct option is (d) E = ln (1 – P)

Best EXPLANATION: For values less than 0.05, E = P. The choice of a < 10-20 SCORE is a conservative one for IDENTIFICATION of orthologs that should have a similar DOMAIN structure.

Right answer is (b) INTRONS of VARYING length and number

The best I can explain: In S. cerevisiae (budding yeast), only a small fraction of the genes contain introns, and there are a total of 239 introns in the entire GENOME. In contrast, in individual human genes, introns may be present in NUMBERS exceeding 100 and COMPRISE more than 95% of the gene.

Correct option is (b) False

To explain I would say: Centromeres hold newly replicated daughter CHROMOSOMES together. They serve as a point of ATTACHMENT for pulling the chromosomes APART during CELL division.

Correct OPTION is (a) Hemophilus influenzae

Explanation: This project was CARRIED out at the Institute of GENOMICS Research. It was carried out in PART to prove a new GENOME sequencing method—the shotgun method.

Right option is (b) Each character is stored in binary CODE in the smallest unit of memory, called a byte

Explanation: Each byte comprises 8 bits, with each bit having a POSSIBLE VALUE of 0 or 1, producing 255 possible combinations. Some ASCII values are defined as keyboard characters, others as special control characters, such as signaling the end of a LINE (a line feed and a carriage return), or the end of a FILE full of text (end-of-file character). A file with only ASCII characters is called an ASCII file.

Right option is (a) True

The explanation: However, these MOLECULES are too large for direct sequencing. One PROCEDURE for sequencing these clones is to subclone them further into smaller fragments that are of SIZES SUITABLE for sequencing, make a map of these clones and then sequence overlapping clones. However, this method is EXPENSIVE because it requires a great deal of time to keep track of all the subclones.

Correct CHOICE is (b) A neighbor-joining algorithm is rarely used in this method

For explanation I would say: The matrix is then used to cluster the sequences by a neighbor-joining algorithm. These methods produce a tree or a different REPRESENTATION of the tree CALLED a dendrogram, which MINIMIZES the number of amino ACID changes that would generate the group of sequences.

The correct OPTION is (B) Eu/Hetero-chromatin STRUCTURES

The best explanation: Option Eu/Hetero-chromatin structures indicate structural studies. Also as mentioned, analysis of the prediction of CHROMOSOMAL rearrangements that preceded the present arrangement is done (e.g., a comparison of mouse and human chromosomes).

The correct ANSWER is (d) one-sixth, one-third

To explain: Hence, in the euchromatic regions, the gene density in the Drosophila GENOME is one gene per 9 kb. DESPITE the fact that the lower number of predicted genes in Drosophila is smaller than that of the other genomes, the amount of functional DIVERSITY, as evidenced by protein family representation, is SIMILAR.

Right ANSWER is (d) increase, large

Explanation: It is a feature already observed in MANY plants and animals. They remain detectable in the GENOME until they blend into the background SEQUENCE by mutation.

Right CHOICE is (c) Synechocystis sp. – Archaea

For explanation: Synechocystis sp. – Bacteria is the CORRECT PAIR. It is an ancient organism that PRODUCES OXYGEN by light-harvesting.

Right answer is (a) True

The best I can explain: When the number of matching sequences has been NARROWED to a REASONABLE number, the SEQUENCE may be retrieved in a CHOSEN FORMAT in several straightforward steps. This helps in getting to the required data in less number of steps.

The CORRECT choice is (a) True

The best I can explain: The format is quite similar to the EMBL format, EXCEPT that considerably more information about the physical and biochemical PROPERTIES of the protein is provided. Also, the OUTPUT of a DDBJ DNA SEQUENCE entry is almost identical to that of GenBank.