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Correct OPTION is (b) False

Best explanation: The EUKARYOTIC transcription initiation requires cooperation of a large number of transcription factors. Co-operativity means that the promoter REGIONS TEND to contain a high density of protein-binding sites. Thus, finding a cluster of transcription FACTOR binding sites often enhances the probability of individual binding site prediction.

Right answer is (c) The CONSERVATION from CLOSELY related ORGANISMS is most at the SEQUENCE level

To explain: The identification of conserved noncoding DNA elements that serve crucial functional roles is REFERRED to as phylogenetic footprinting; the elements are called phylogenetic footprints. This type of method can apply to both prokaryotic and eukaryotic sequences.

Right answer is (a) It is a program that PREDICTS promoters for BACTERIAL DNA

To elaborate: It uses quadratic discriminant functions (see CHAPTER 8) to calculate the probabilities of the first exon of a gene and its boundary sites. A segment of DNA (15 kb) upstream of the first exon is subsequently EXTRACTED for promoter prediction on the basis of SCORES for CpG islands.

Right answer is (c) It works by detecting a region of high concentration of unknown transcription factor binding sites and regulatory motifs at the initiation

To EXPLAIN: It works by detecting a region of high concentration of known transcription factor binding sites and regulatory motifs. If multiple motifs are detected within a window, a positive score is assigned to each motif found. The TOTAL score of the window is the SUM of each motif score SUBTRACTING a gap penalty, which is proportional to the distances between motifs. If the score of a certain region is above a certain threshold, it is predicted to contain a regulatory cluster.

The correct choice is (a) True

For explanation I would say: The predictive VALUE of this method also depends on the quality of the subsequent sequence alignments. Advanced ALIGNMENT programs can be used. Even more SOPHISTICATED expectation maximization (EM) and Gibbs sampling algorithms can be used in DETECTING weakly conserved MOTIFS.

The correct answer is (a) True

The best I can explain: rVISTA is a cross-species COMPARISON tool for PROMOTER RECOGNITION. It aligns the two sequences using a local alignment strategy. The motifs that have the highest percent identity in the pairwise comparison are presented GRAPHICALLY as REGULATORY elements.

The CORRECT option is (b) It is a web-based program that particularly predicts tranpososons and retropososons

The explanation is: The query sequence from a mammalian source is scanned through the PSSMs. The sequence stretches with high-score matching to all the PSSMs, as WELL as matching of the spacing between the ELEMENTS, are declared transcription start SITES. A Bayesian method is also used in DECISION making.

Correct choice is (a) True

For explanation I would say: It is known that many vertebrate genes are characterized by a HIGH density of CG dinucleotides near the promoter region overlapping the transcription start SITE. By identifying the CpG islands, promoters can be traced on the immediate upstream region from the islands. By combining CpG islands and other promoter signals, the accuracy of PREDICTION can be IMPROVED. Several programs have been developed BASED on the combined features to predict the transcription start sites in particular.

Right option is (c) cDNA does not PLAY a role in prediction

For explanation: To use the PROGRAM, a user supplies the TRANSCRIPT sequence of a gene (cDNA). It then uses the GENSCAN program to predict 5’ untranslated exons in the UPSTREAM region. Once the 5’-most exon is located, a further upstream region (1.5 kb) is used for promoter prediction, which relies on a combination of five promoter prediction programs, TSSG, TSSW, NNPP, PROSCAN, and PromFD.

Correct option is (b) The method GENERATES a single best alignment

Easiest explanation: Instead of returning a single best alignment, the method generates a distribution of a large number of alignments using a full range of scoring matrices and gap PENALTIES. By studying the distribution, the alignment that has the HIGHEST likelihood score, which is in the EXTREME margin of the distribution, is chosen. Based on this unique alignment searching algorithm, weakly conserved motifs can be identified with high probability SCORES.

The correct answer is (c) The PROGRAM does not accept pre-computed alignment

The best explanation: The USER provides two individual sequences which are aligned by ConSite using a global alignment algorithm. Conserved REGIONS are identified by calculating identity scores, which are then used to compare against a motif database of REGULATORY sites (TRANSFAC). High-scoring sequence segments upstream of genes are returned as putative regulatory elements.

Correct choice is (b) This APPROACH appears to be less effective for finding TRANSCRIPTION factor binding sites

The explanation is: This approach is essentially experimentally based and appears to be robust for finding transcription factor binding sites. The problem is that the regulatory ELEMENTS of coexpressed genes are usually short and weak. Their patterns are difficult to discern USING simple multiple SEQUENCE alignment approaches.

Correct choice is (a) True

The EXPLANATION: If three predictions fall within a 100-bp region, this is considered a CONSENSUS prediction If no three-way consensus is achieved, TSSG and PromFD predictions are TAKEN. Because no coding sequence is USED in prediction, specificity is improved RELATIVE to each individual program.

Correct OPTION is (a) True

For explanation I would say: As mentioned here, TSSW uses unique content information such as hexamer/trimer frequencies and signal information such the TATA box in the promoter region. The values are fed to a linear DISCRIMINANT FUNCTIONTO separate true motifs from background noise.

Right choice is (d) Signals such as CpAA islands

The best I can explain: As seen, the correct answer is CpG in option d. The hidden layer combines all the FEATURES to DERIVE an overall likelihood for a site being a promoter. Another unique feature is that McPromoter does not require that certain patterns MUST be present, but instead the combination of all features is important. For instance, even if the TATA box SCORE is very low, a promoter prediction can still be MADE if the other features score highly. The program is currently trained for Drosophila and human sequences.

The correct choice is (a) True

Easy explanation: The pipeline processes microarray data, automatically clusters genes according expression patterns, retrieves upstream sequences of coregulated genes and detects motifs USING a Gibbs sampling approach (Motif Sampler). To further avoid the PROBLEM of GETTING stuck in a local OPTIMUM, each sequence dataset is SUBMITTED to Motif Sampler ten times. The results may vary in each run. The results from the ten runs are compiled to derive consensus motifs.

Correct answer is (a) only the first GENE is PREDICTED, WHEREAS other genes

Best explanation: Only the first gene is predicted for the PRESENCE of a promoter and REGULATORY elements, whereas other genes in the operon do not possess such DNA elements. There are a number of methods available for prokaryotic operon prediction. The most accurate is a set of simple rules developed.

Right choice is (a) MEME is the EM based program only for PROTEIN motif discovery

Easiest explanation: The use of MEME is similar to that for protein sequences and DNA motif finding. AlignACE automatically DETERMINES the optimal NUMBER and LENGTHS of motifs from the input sequences. Melina is a web-based program that runs four individual motif-finding algorithms – MEME, GIBBS sampling, CONSENSUS, and Core search – simultaneously. The user COMPARES the results to determine the consensus of motifs predicted by all four prediction methods.

Correct answer is (a) True

To explain: In addition, many genes have a unique initiator SEQUENCE (Inr), which is a pyrimidine rich sequence with a consensus (C/T)(C/T)CA(C/T)(C/T). This site coincides with the transcription start site. Most of the transcription factor binding sites are LOCATED within 500 bp upstream of the transcription start site.

The correct answer is (d) exclude, (0.5 to 2.0 kb) only

To explain I would say: To better discriminate true MOTIFS from background noise, a NEW generation of algorithms has been developed that take into account the higher order CORRELATION of multiple subtle features by using discriminant functions, neural networks, or hidden Markov models (HMMs) that are capable of incorporating more neighboring sequence information.

Correct answer is (a) True

To explain: The most bacterial promoters are located within 200 bp of the PROTEIN coding REGION. HENCE, the program is most effectively used when about 200 bp of upstream sequence of the FIRST gene of an operon is supplied as input to increase specificity.

The correct answer is (a) True

Best explanation: The core of many eukaryotic PROMOTERS is a so-called TATA box, LOCATED 30 bps upstream from the transcription start site, having a consensus motif TATA (A/T) A (A/T). HOWEVER, not all eukaryotic promoters contain the TATA box. Many GENES such as housekeeping genes do not have the TATA box in their promoters.

Right option is (d) Synthesis of mRNAs is CARRIED out by RNA polymerase I

The explanation is: Ach polymerase TRANSCRIBES different SETS of GENES. RNA polymerase II is exclusively responsible for transcribing protein-encoding genes or synthesis of mRNAs.

Correct answer is (a) True

The explanation is: The LIMITATION is the NEED for TRAINING, which makes the prediction programs species specific. In addition, this TYPE of method has a difficulty in discovering new, unknown motifs.

Right answer is (a) True

For explanation: This includes the sequence segments located 35 and 10 base pairs (bp) UPSTREAM from the transcription start site. They are also referred to as the −35 and −10 BOXES. For the σ70 subunit in Escherichia coli, for example, the −35 BOX has a CONSENSUS sequence of TTGACA. The –10 box has a consensus of TATAAT.

Right answer is (a) It relies on two kinds of INFORMATION: gene orientation and intergenic distances of a pair of GENES of interest and conserved linkage of the genes based on comparative genomic analysis

Best explanation: A scoring scheme is developed to assign operons with different levels of Confidence. This method is claimed to produce accurate identification of an operon structure, which in turn facilitates the promoter prediction. The prediction can be DONE manually using the rules. The few dedicated programs for prokaryotic promoter prediction do not apply the rule for historical reasons. The most FREQUENTLY used program is BPROM.

Right option is (d) The consensus sequences or the matrices are relatively large, covering 700 to 1000 bases

Easiest explanation: To determine whether a query SEQUENCE matches a weight matrix, the sequence is scanned through the matrix. Scores of matches and mismatches at all matrix positions are summed up to give a log odds score, which is then evaluated for statistical significance. This simple approach, however, OFTEN has difficulty differentiating true promoters from random sequence matches and generates HIGH rates of false positives as a result.

The correct option is (a) True

Best explanation: In the latter CASE, the linked genes form an OPERON. It is controlled by the PROMOTER.

Right option is (d) regulatory elements

Explanation: The regulatory elements may bind in the vicinity of the promoter or bind to a SITE several HUNDRED bases away from the promoter. The reason that the binding of the regulatory protein at long distance can still exert their effect is because of the flexible structure of DNA, which is able to BEND and exert its effect by bringing the transcription factors in close contact with the RNA polymerase COMPLEX.

Correct choice is (b) False

Easy EXPLANATION: In bacteria, transcription is INITIATED by RNA polymerase, which is a multi-subunit ENZYME. The σ subunit (e.g., σ70) of the RNA polymerase is the protein that recognizes specific sequences upstream of a gene and allows the rest of the enzyme COMPLEX to bind.

The correct option is (B) It is a web-based program only for prediction of eukarotic promoters

To explain I would say: The linear discriminant function is combined with signal and content INFORMATION such as consensus promoter sequence and oligonucleotide composition of the promoter sites. This program first predicts a given sequence for bacterial operon STRUCTURES by using an intergenic distance of 100 bp as basis for distinguishing genes to be in an operon.

Correct answer is (a) The consensus patterns are only DERIVED from BIOINFORMATICS studies

The explanation is: This APPROACH tends to generate very high rate of false positives owing to nonspecific matches with the short sequence patterns. Furthermore, because of the high variability of transcription factor binding sites, the simple sequence matching often misses TRUE promoter sites, creating false NEGATIVES.