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The correct option is (a) True

Explanation: HEURISTICS such as BLAST and FASTA are developed for faster speed. However, the heuristic METHODS are limited in SENSITIVITY and are not GUARANTEED to find the optimal alignment. They often fail to find alignment for distantly related sequences.

The correct option is (b) False

For explanation I WOULD say: The speed is the TIME it takes to get results from database searches. Depending on the size of the database, speed sometimes can be a PRIMARY concern in the SEARCH methods.

The correct CHOICE is (a) True

For explanation I would say: Among the unique requirements for implementing algorithms for sequence database Searching, the FIRST criterion is sensitivity, which REFERS to the ability to FIND as many correct hits as possible. It is MEASURED by the extent of inclusion of correctly identified sequence members of the same family. These correct hits are considered ‘true positives’ in the database searching exercise.

Right option is (d) subtracting, first, second

Easiest explanation: The positional difference for each word between the two SEQUENCES is OBTAINED by subtracting the POSITION of the first sequence from that of the second sequence and is EXPRESSED as the offset. The ktups that have the same offset values are then linked to reveal a contiguous IDENTICAL sequence region that corresponds to a stretch of diagonal in a two-dimensional matrix.

The CORRECT answer is (B) False

To explain: Negative score is SET to 0. In Needleman–Wunsch ALGORITHM, the Score can be negative. ALSO, in Smith–Waterman algorithm, in tracing back step, it begins with the highest score, ends when 0 is encountered.

Right option is (B) False

For explanation I would say: The DIAGONAL’s nature indicates the matching of the SEQUENCES. After all diagonals are found, it tries to JOIN diagonals by adding gaps. Further, it COMPUTES alignments in regions of best diagonals.

Correct answer is (a) True

Explanation: The results of the word MATCHING and attempts to extend the alignment are segments. They are called as HSPs (High-Scoring Segment PAIRS). BLAST often PRODUCES SEVERAL SHORT HSPs rather than a single aligned region.

Correct answer is (d) TBLASTNX

Explanation: BLAST is a family of programs that includes BLASTN, BLASTP, BLASTX TBLASTN, and TBLASTX. BLASTN queries nucleotide sequences with a nucleotide sequence database. The alignment scoring is BASED on the BLOSUM62 matrix.

The correct option is (a) >

The best explanation: Its FORMAT is simple as used by almost all programs. Header line has > at the beginning. ALSO no specific requirements are there for line length, CHARACTERS, etc.

The CORRECT answer is (c) significant, certainty

To elaborate: If Z is in the range of 5 to 15, the sequence pair can be DESCRIBED as highly probable homologs. If Z<5, their relationship is described as less CERTAIN.

Right option is (b) False

The explanation: TBLASTN queries protein sequences to anucleotide SEQUENCE database with the sequences translated in all six reading frames. TBLASTX uses nucleotide sequences, which are translated in all six frames, to search against a nucleotide sequence database that has all the sequences translated in six frames. In addition, there is also a bl2seq program that performs local alignment of two user-provided input sequences. The graphical OUTPUT INCLUDES horizontal bars and a diagonal in a two-dimensional diagram SHOWING the OVERALL extent of matching between the two sequences.

Correct choice is (c) decrease

To explain I would say: Ideally, one wants to have the GREATEST sensitivity, selectivity, and speed in database searches. However, satisfying all three requirements is DIFFICULT in reality. What generally happens is that an increase in sensitivity is associated with decrease in selectivity. A very inclusive search tends to include many false POSITIVES. Similarly, an improvement in speed often comes at the cost of lowered sensitivity and selectivity. A compromise between the three criteria often has to be made.

The correct choice is (b) False

For explanation: DYNAMIC programming method is SLOW and impractical to USE in most cases. Special SEARCH METHODS are needed to speed up the computational process of sequence comparison.

Right answer is (a) True

Best EXPLANATION: In addition to the given STATEMENT, BLAST SOMETIMES gives MULTIPLE best-scoring ALIGNMENTS from the same sequence. FASTA returns only one final alignment.

Correct option is (a) True

Easiest EXPLANATION: This process involves submission of a query SEQUENCE and PERFORMING a pairwise comparison of the query sequence with all individual sequences in a database. THUS, database similarity searching is pairwise alignment on a large scale. This type of searching is one of the most effective ways to assign putative functions to newly DETERMINED sequences.

The correct option is (b) False

For EXPLANATION I would say: In heuristic DATABASE searching methods, The SECOND requirement criterion is 1 also called specificity, which refers to the ability to exclude incorrect hits. These incorrect hits are UNRELATED sequences mistakenly identified in database searching and are considered ‘false POSITIVES.’

Correct answer is (a) True

To explain: Because most of the alignments with the query sequence are with unrelated sequences, the higher the Z-score for a reported match, the further away from the mean of the score distribution, hence, the more significant the match. For a Z-score > 15, the match can be considered extremely significant, with a CERTAINTY of a homologous relationship. If Z is in the range of 5 to 15, the sequence pair can be described as highly probable homologs. If Z<5, their relationship is described as less CERTAIN.

Correct choice is (a) True

Easy explanation: The heuristic subprogram first finds exact ungapped alignments and uses them as anchors for extension into gapped alignments by combining the SCORES of SEVERAL diagonals in the alignment MATRIX. The search speed of ParAlign approaches to that of BLAST, but with higher sensitivity.

The correct OPTION is (a) True

Best EXPLANATION: These methods are not guaranteed to find the optimal alignment or true homologs, but are 50–100 times faster than dynamic programming. The increased computational speed COMES at a moderate expense of sensitivity and specificity of the SEARCH, which is easily tolerated by working molecular biologists. Both programs can provide a REASONABLY good indication of sequence similarity by identifying similar sequence segments.

Right OPTION is (b) False

Explanation: ScanPS (Scan Protein Sequence) is a web-based PROGRAM that implements a modified version of the Smith–Waterman algorithm optimized for parallel processing. The MAJOR feature is that the program allows iterative searching similar to PSI-BLAST, which builds profiles from one round of search results and uses them for the second round of database searching. Full dynamic programming is used in each cycle for ADDED sensitivity.

The CORRECT CHOICE is (a) Handling of gaps

For explanation: In addition to this, user friendly UI of BLAST is ALSO one of its benefits. HOWEVER, it does not handle gaps well. In that case gapped BLAST is better.

The CORRECT CHOICE is (a) True

The explanation: It can ALSO be USED for modular organization of genes and proteins (exons, domains, etc.) Also it can be used in cases of sequences diverged so that similarity was retained, or can be detected, just in some sub-regions.

Correct choice is (b) False

To explain I would say: FASTA uses E-values and bit scores as well. Estimation of the TWO PARAMETERS in FASTA is ESSENTIALLY the same as in BLAST. HOWEVER, the FASTA output provides one more statistical parameter, the Z-score.

The CORRECT answer is (a) first, first

The explanation: In Smith–Waterman ALGORITHM, first ROW and first column are set to 0. In the Needleman Wunsch algorithm, First row and first column are subject to gap PENALTY.

The CORRECT option is (a) True

The best explanation: Similar to BLAST, FASTA has a number of subprograms. The web-based FASTA program offered by the European Bioinformatics INSTITUTE ALLOWS the use of either DNA or protein sequences as the QUERY to search against a protein database or nucleotide database.

The correct option is (a) True

The explanation: In gapped BLAST, the HIGHEST scored segment is chosen to be extended in both directions using dynamic programming where gaps may be introduced. The EXTENSION continues if the alignment score is above a certain THRESHOLD; otherwise it is terminated. However, the overall score is ALLOWED to drop below the threshold only if it is temporary and rises again to attain above threshold values. Final trimming of terminal regions is needed before producing a report of the final alignment.

The correct option is (c) THREE, eleven

For explanation: The FIRST STEP is to create a list of words from the QUERY sequence. Each word is typically three residues for protein sequences and eleven residues for DNA sequences. The list includes every possible word extracted from the query sequence. This step is also CALLED seeding.

Correct option is (a) True

Best EXPLANATION: It is because mutations have added too much ‘NOISE’ over evolutionary time to ALLOW for a meaningful comparison of those regions. Local alignment AVOIDS such regions ALTOGETHER and focuses on those with a positive score, i.e. those with an evolutionarily conserved signal of similarity.

Correct option is (B) faster, less sensitive

Easy explanation: Empirical tests have indeed shown that the exhaustive METHOD PRODUCES superior results over the heuristic methods like BLAST and FASTA. But heuristic methods are better and PRACTICAL when it comes to assess larger datasets with comparatively low sensitivity.

The correct ANSWER is (a) True

For explanation I WOULD say: The LAST step of FASTA is similar to that of BLAST. The determination of E-value is the most important part of the whole analysis as it gives the degree of alignment between the SEQUENCES.

Correct choice is (a) True

The EXPLANATION: This step is to identify database sequences containing the MATCHING words. The matching of the words is SCORED by a GIVEN substitution matrix. A word is considered a match if it is above a THRESHOLD.

The correct choice is (a) Smith–Waterman algorithm is the fastest

For explanation: Searching a LARGE DATABASE using the dynamic programming methods, such as the Smith–Waterman algorithm, ALTHOUGH accurate and reliable, is too slow and impractical when computational resources are limited. To speed up the comparison, heuristic methods have to be used. The heuristic algorithms perform faster searches because they examine only a fraction of the possible ALIGNMENTS EXAMINED in regular dynamic programming.

The correct option is (c) It gives less sensitive results

To EXPLAIN I WOULD say: By default, FASTA scans SMALLER window SIZES. Thus, it gives more sensitive results than BLAST, with a better coverage rate for homologs. However, it is usually slower than BLAST.

Right option is (a) True

To explain I would SAY: Normally, MANY diagonals between the two SEQUENCES can be identified in the hashing STEP. The top ten regions with the highest density of diagonals are identified as high SIMILARITY regions. The diagonals in these regions are scored using a substitution matrix.

The CORRECT choice is (a) substitution matrix, HASHING procedure

Easy explanation: BLAST and FASTA have been shown to perform almost equally well in regular DATABASE searching; However, there are some NOTABLE differences between the two approaches. The major difference is in the seeding step– BLAST uses a substitution matrix to find matching words, whereas FASTA identifies identical matching words using the hashing procedure.

Correct option is (c) 1990

Easiest EXPLANATION: The BLAST program was DEVELOPED by Stephen Altschul of NCBI in 1990 and hassince become one of the most popular programs for SEQUENCE analysis. BLAST uses heuristics to align a query sequence with all SEQUENCES in a database.

The correct option is (a) True

The explanation is: This step allows INTRODUCING gaps between the diagonals while applying gap penalties. The score of the gapped alignment is calculated again. In step 3, the gapped alignment is refined further using the Smith–Waterman ALGORITHM to PRODUCE a final alignment.

Correct answer is (d) The string of residues is known as blocks

The explanation: The string of residues is known as ktuples or ktups, which are EQUIVALENT to words inBLAST, but are normally shorter than the words. Typically, a ktup is composed of TWO residues for PROTEIN sequences and six residues for DNA sequences.

Correct answer is (a) Size of the dataset

For explanation I would say: There are unique requirements for IMPLEMENTING algorithms for sequence database SEARCHING out of which, the LATER three play an important role. HOWEVER, speed can vary with the size of database. ACHIEVING all three at a time is nearly impossible.

Correct answer is (a) True

BEST explanation: Because of this, it computes best diagonals from all frames of ALIGNMENT. The method LOOKS for EXACT matches between words in query and test sequence.

Right option is (d) TWO related sequences must have at zero word in common while assuming

Explanation: This is the third method of pairwise sequence alignment. It works by finding SHORT stretches of identical or nearly identical letters in two sequences. These short strings of characters are called words, which are similar to the windows used in the DOT matrix method. The basic assumption is that two related sequences must have at least one word in common. By FIRST identifying word matches, a longer alignment can be obtained by EXTENDING similarity regions from the words. Once regions of high sequence similarity are found, adjacent high-scoring regions can be joined into full alignment.

Correct choice is (a) True

The BEST explanation: In BLAST, SIMILARITY matching of words is involved. If no words are found SIMILAR, then no alignment is detected and HENCE it might not find matches for very short sequences.