Q. One of the challenges in SWA is obtaining correct alignments in regions of low similarity between distantly related biological sequences.

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Q. In SW algorithm, to align two sequences of lengths of m and n _________ time is required.

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Q. Local sequence alignments are necessary for many cases out of which one is repeated.

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Q. In Smith–Waterman algorithm, in initialization Step, the _________ row and ________ column are subject to gap penalty.

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Q. Par Align is a web-based server that uses parallel processors to perform exhaustive sequence comparisons using either a parallelized version of the Smith–Waterman algorithm or a heuristic program for further speed gains.

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Q. Scan PS is a web-based program that implements a modified version of the Needleman-Wunsch algorithm.

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Q. FASTA and BLAST are __________ but __________ for larger datasets.

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Q. The rigorous dynamic programming method is normally not used for database searching because it is slow and computationally expensive.

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Q. The initiation of FASTA format has ____ symbol.

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Q. The gapped portion in the diagonals represents matches in FASTA.

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Q. FASTA is derived from logic of the dot plot.

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Q. BLAST often produces several short HSPs rather than a single aligned region.

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Q. BLAST might not find matches for very short sequences.

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Q. Which of the following is not a benefit of BLAST?

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Q. The use of low-complexity masking in the BLAST procedure means that it may have higher specificity than FASTA because potential false positives are reduced.

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Q. Which of the following is not a benefit or a factual of FASTA over BLAST?

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Q. BLAST uses a _______ to find matching words, whereas FASTA identifies identical matching words using the _____

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Q. In FASTA, For a Z-score > 15, the match can be considered extremely ______ with _____ of a homologous relationship.

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Q. Z-score describes the number of standard deviations from the mean score for the database search.

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Q. FASTA doesn’t use bit scores.

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