This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “FASTA”.
1. Which of the following is not correct about FASTA?
a) Its stands for FAST ALL
b) It was in fact the first database similarity search tool developed, preceding the development of BLAST
c) FASTA uses a ‘hashing’ strategy to find matches for a short stretch of identical residues with a length of k
d) The string of residues is known as blocks
View Answer
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.
2. The first step in FASTA alignment id to arrange the sequences in matrices’ rows and columns in order to be analyzed.
a) True
b) False
View Answer
Explanation: The first step in FASTA alignment is to identify ktups between two sequences by using the hashing strategy. This strategy works by constructing a look up table that shows the position of each ktup for the two sequences under consideration. The mentioned method is similar to that of BLAST.
3. The positional difference for each word between the two sequences is obtained by ________ the position of the ______ sequence from that of the _______ sequence and is expressed as the offset.
a) subtracting, second, first
b) adding, second, first
c) adding, first, second
d) subtracting, first, second
View Answer
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.
4. The second step in FASTA is to narrow down the high similarity regions between the two sequences.
a) True
b) False
View Answer
Explanation: 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.
5. In FASTA, neighboring high-scoring segments along the same diagonal are selected and joined to form a single alignment.
a) True
b) False
View Answer
Explanation: 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.
6. The last step is to perform a statistical evaluation of the final alignment as in BLAST, which produces the E-value.
a) True
b) False
View Answer
Explanation: 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.
7. The web-based FASTA program is offered by the European Bioinformatics Institute.
a) True
b) False
View Answer
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.
8. FASTX, which compares a protein query sequence to a translated DNA database.
a) True
b) False
View Answer
Explanation: Some available variants of the program are FASTX and TFASTX. FASTX translates a DNA sequence and uses the translated protein sequence to query a protein database. TFASTX compares a protein query sequence to a translated DNA database.
9. FASTA doesn’t use bit scores.
a) True
b) False
View Answer
Explanation: 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.
10. Z-score describes the number of standard deviations from the mean score for the database search.
a) True
b) False
View Answer
Explanation: 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.
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