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Right choice is (C) The alignment is rarely done using a dynamic programming–based algorithm

To explain I would say: The alignment is done using dynamic programming–based algorithm. Another advantage is that there is no need for model training, which provides much more flexibility for gene prediction. The limitation is that EST or cDNA SEQUENCES OFTEN contain errors or even introns if the TRANSCRIPTS are not completely spliced before reverse transcription.

Correct choice is (a) True

For explanation I would say: It COMBINES hexamer frequencies with coding signals (initiation CODONS, TATA box, cap site, poly-A, etc.) in prediction. Putative exons are assigned a probability score (P) of being a true exon. Only predictions with P > 0.5 are deemed RELIABLE. This PROGRAM is trained for sequences from VERTEBRATES, Arabidopsis, and maize. It has been used extensively in annotating the human genome.

Correct ANSWER is (a) True

The explanation: These can be REPRESENTED with various orders of Markov models. Since a fixed-order Markov chain describes the probability of a particular nucleotide that DEPENDS on previous k nucleotides, the longer the oligomer unit, the more non-randomness can be DESCRIBED for the coding region. Therefore, the higher the order of a Markov MODEL, the more accurately it can predict a gene.

Right OPTION is (b) does not necessarily

To explain I would say: Because there may be multiple ATG, GTG, or TGT codons in a frame, the presence of these codons at the beginning of the frame does not necessarily GIVE a clear indication of the translation initiation site. Instead, to HELP identify this initiation codon, other features associated with translation are USED.

Correct answer is (a) True

Easiest explanation: It has been observed that NUCLEOTIDE composition and statistical PATTERNS of the coding regions tend to vary SIGNIFICANTLY from those of the non-coding regions. The UNIQUE features can be detected by employing probabilistic models such as Markov models or hidden Markov models to HELP distinguish coding from non-coding regions.

Correct choice is (a) They are based on the fact that EXON STRUCTURES and exon sequences of related species are less conserved

Explanation: Homology-based programs are based on the fact that exon structures and exon sequences of related species are highly conserved. When POTENTIAL coding frames in a QUERY sequence are translated and used to align with closest protein homologs FOUND in databases, near perfectly matched regions can be used to reveal the exon boundaries in the query.

The CORRECT choice is (b) Prokaryotes have relatively large genomes

The best I can explain: Prokaryotes have relatively small genomes with sizes RANGING from0.5 to 10Mbp (1Mbp=106 bp). Each prokaryotic gene is COMPOSED of a SINGLE contiguous stretch of ORF CODING for a single protein or RNA with no interruptions within a gene.

The CORRECT choice is (c) HMM prediction is unbiased toward the LOCKED region

Best explanation: An HMM prediction is subsequently made with a bias toward the locked region and is extended from the locked region to predict the rest of the GENE CODING regions and even neighboring genes. The program is in a way a hybrid algorithm that uses both ab initio-based and homology-based CRITERIA.

Correct answer is (a) True

For explanation: These programs work by retaining common predictions agreed by most programs and removing inconsistent predictions. Such an integrated APPROACH may IMPROVE the specificity by correcting the false positives and the PROBLEM of over prediction. However, since this procedure punishes novel predictions, it may lead to lowered sensitivity and MISSED predictions.

Correct answer is (c) The second event is SPLICING, which is the process of removing exons and joining introns

To elaborate: The reaction requires intermolecular interactions between a pair of nucleotides at each end of an intron and the RNA component of the spliceosome. To MAKE the matter EVEN more complex, some eukaryotic genes can have their transcripts spliced and joined in different WAYS to generate more than one transcript per gene. This is the phenomenon of alternative splicing.

Right option is (a) True

Easy explanation: Among these features, the hexamer frequencies appear to be most discriminative for coding potentials. To derive an assessment for this FEATURE, HMMscan be used, which require proper training. In ADDITION to HMMs, neural network-based ALGORITHMS are also common in the GENE prediction field.

Right OPTION is (a) True

The best I can EXPLAIN: The putative EXONS are used for BLAST searching to find closest homologs. The putative exons and homologs from BLAST searching are aligned to identify the best match. Only the closest match from a genome database is used as a template for refining the previous exon selection and exon boundaries.

The correct choice is (a) True

For explanation: If the homologs are not available in the DATABASE, the method cannot be USED. NOVEL genes in a new SPECIES cannot be discovered without matches in the database. A number of publicly available programs USE this approach.

The CORRECT answer is (b) They tend to have a very high gene density

To elaborate: In HUMANS, for instance, only 3% of the genome codes for genes, with about 1 gene PER 100 kbp on average. The space between genes is OFTEN very LARGE and rich in repetitive sequences and transposable elements.

Right option is (b) Prokaryotic DNA is first subject to conceptual translation in all six possible frames, two frames forward and four frames reverse

Easy explanation: Prokaryotic DNA is first subject to conceptual translation in all six possible frames, three frames forward and three frames reverse. Because a stop CODON occurs in about every twenty codons by chance in a noncoding region, a frame LONGER than thirty codons without interruption by stop codons is suggestive of a GENE coding region, although the threshold for an ORF is normally set EVEN higher at fifty or SIXTY codons.

The correct choice is (d) It does not MAKE a use of HMMs

The best explanation: In addition to FGENES, there are MANY variants of the program. Some programs, such as FGENESH, make use of HMMs. There are others, such as FGENESH C, that are SIMILARITY BASED. Some programs, such as FGENESH+, combine both ab initio and similarity-based APPROACHES.

The correct OPTION is (a) True

The explanation is: The program SCANS the query SEQUENCE with windows of variable lengths and scores for coding potentials and FINALLY produces an output that is the result of exon candidates. The program is currently trained for human, mouse, Arabidopsis, Drosophila, and Escherichia coli sequences.

Correct OPTION is (d) THREE

The explanation is: At the end of the PROTEIN coding region is a stop codon that causes translation to stop. There are three possible stop codons, identification of which is straightforward. Many prokaryotic genes are transcribed TOGETHER as ONE operon.

The correct answer is (a) True

To explain I would say: Occasionally, GTG and TTG are used as alternative start CODONS. But methionine is STILL the actual AMINO acid inserted at the first POSITION.

The CORRECT choice is (a) True

The explanation is: These statistical methods, which are based on EMPIRICAL rules, examine the statistics of a SINGLE nucleotide (either G or C). To improve the PREDICTION accuracies, the new generation of prediction algorithms uses more sophisticated statistical MODELS.

Right choice is (c) A GeneMark heuristic program can be USED to improve accuracy

Best explanation: Another option for PREDICTING genes from a new ORGANISM is to use a self-trained program GeneMarkS as long as the user can provide at least 100 KBP of sequence on which to train the model. If the query sequence is shorter than 100 kbp, a GeneMark heuristic program can be used with some loss of accuracy. In addition to predicting prokaryotic genes, GeneMark ALSO has a variant for eukaryotic gene prediction using HMM.

The correct choice is (b) ATG

To explain: In addition, most of these genes have a high density of CG DINUCLEOTIDES near the transcription start SITE. This REGION is referred to as a CPG island (p refers to the phosphodiester bond connecting the two nucleotides), which helps to identify the transcription initiation site of a eukaryotic gene. The poly-A signal can also help locate the final CODING sequence.

Correct choice is (a) True

Explanation: The user PROVIDES genomic DNA and PROTEIN sequences from related species. The genomic DNA is translated in all six frames to cover all possible exons. The translated exons are then USED to compare with the user-supplied protein sequences.

Correct answer is (a) True

Easy EXPLANATION: From a computational point of view, it is a very complex and challenging problem. Because of the PRESENCE of split GENE structures, alternative SPLICING, and very low gene densities, the difficulty of finding GENES in such an environment is likened to finding a needle in a haystack.

Correct option is (c) In a Markov MODEL the conditional probability of a particular sequence position depends on k alternate POSITIONS

For explanation: In a Markov model the conditional probability of a particular sequence position depends on k previous positions. In this case, k is the order of a Markov model. In a zero-order Markov model, it is often the case for noncoding SEQUENCES. A first-order Markov model ASSUMES that the occurrence of a base depends on the base preceding it. A second-order model LOOKS at the preceding two bases to determine which base follows, which is more characteristic of codons in a coding sequence.

The correct ANSWER is (d) To predict exons, the algorithms rely solely on gene signals

Easiest explanation: To predict exons, the algorithms rely on two FEATURES, gene signals and gene content. Signals include gene start and stop sites and putative SPLICE sites, recognizable consensus SEQUENCES such as poly-A sites.

Right option is (d) LDA works by plotting a three-dimensional graph of coding signals versus all potential 3’ splice site positions

Explanation: QDA draws a curved line BASED on a quadratic function instead of drawing a STRAIGHT line to separate coding and noncoding features. This STRATEGY is designed to be more flexible and provide a more optimal separation between the data POINTS.

Correct choice is (c) The model is not fed with a SEQUENCE of known gene structure

To explain: Between input and output, there MAY be one or SEVERAL hidden layers where the machine learning takes place. The machine learning process starts by feeding the model with a sequence of known gene structure. The gene structure information is separated into several classes of features such as HEXAMER frequencies, splice sites, and GC composition during training. The weight functions in the hidden layers are adjusted during this process to recognize the NUCLEOTIDE patterns and their relationship with known structures.

Correct option is (d) It exploits the fact that the third codon nucleotides in a coding region fails to REPEAT themselves

Explanation: In a coding SEQUENCE, it has been OBSERVED that this position has a preference to use G or C over A or T. By plotting the GC composition at this position, REGIONS with values significantly above the random level can be identified, which are indicative of the presence of ORFs. This method exploits the fact that the third codon nucleotides in a coding region TEND to repeat themselves.

Correct option is (a) True

Easiest EXPLANATION: It is located immediately downstream of the TRANSCRIPTION initiation site and slightly upstream of the translation start CODON. In many bacteria, it has a CONSENSUS motif of AGGAGGT. Identification of the ribosome binding site can help locate the start codon.

Right option is (a) True

Explanation: They also INCLUDE ribosomal binding SITES, and polyadenylation (poly-A) sites. In addition, the TRIPLET codon structure LIMITS the coding frame length to multiples of three, which can be USED as a condition for gene prediction.

Right option is (c) It is a similarity-based web PROGRAM that aligns two genomic DNA sequences from DISTINCTLY related organisms

Explanation: It aligns two genomic DNA sequences from closely related organisms. Similar to EST2Genome, there is no training NEEDED. The limitation is the need for two homologous sequences having similar genes with similar exon structures; if this condition is not met, a GENE escapes detection from one sequence when there is no counterpart in ANOTHER sequence.

Correct answer is (a) True

The best I can explain: The PARAMETERS of a Markov Model have to be trained using a SET of SEQUENCES with known gene LOCATIONS. Once the parameters of the model are established, it can be used to compute the nonrandom distributions of trimers or HEXAMERS in a new sequence to find regions that are compatible with the statistical profiles in the learning set.

Correct ANSWER is (c) They resembles ab initio approaches

Easy explanation: Aspect of the model that makes it look like a BIOLOGICAL neural network is its ability to “learn” and then make predictions after being trained. The network is able to process information and modify parameters of the weight functions between variables during the TRAINING stage. Once it is trained, it is able to make automatic predictions about the unknown. This is QUITE different than the ab initio METHODS.

The correct option is (c) It does not necessarily usethe IMM algorithm

Best EXPLANATION: The computation consists of two steps, namely model building and gene prediction. The model building involves training by the input sequence, which optimizes the parameters of the model. In an actual gene prediction, the overlapping frames are “flagged” to alert the USER for further inspection. Glimmer also has a variant, GlimmerM, for EUKARYOTIC gene prediction.