Question

Why is it the case that an algorithm such as BLAST or Smith-Waterman is inappropriate for comparing (sequences of) whole genomes? Consider the characteristics of the algorithms, the complexity of the problem of comparing genomes, and the form of results that would be sought by users comparing genomes.

Answer 1

Answer:- when we see the basic principle of both algorithm –

BLAST [basic local alignment tool] and Smith – Wataerman is comparing amino acid or DNA or RNA sequences at local level as opposed to global. These two algorithm give the highest –scoring local match between two sequences. That means only a fractions / segments of two/ more sequences compare rather than full length. These are used to compare the two sequences that have a matched segments of different lengths, that overlap or where one sequence is fragment of other.

Local alignment is the difficulty of obtaining correct alignments in regions of low similarity between distantly related biological sequences, because mutations have added too much 'noise [alteration]’ in the sequence.

•   BLAST is used to detect relationships among sequences that share only isolated region of similarity. But in the different genomes[from two different organism] dissimilar regions are always there, with this algorithm we can’t get comparison of these portion. In BLAST the sequences are compare only with library sequence , and if there is any kind of mutation in our sample sequence, the algorithm not able to detect.

•Smith–Waterman algorithm aligns two sequences by matches/mismatches (also known as substitutions), insertions, and deletions. Both insertions and deletions are the operations that introduce gaps, which are represented by dashes. That why we can’t compare two sequences and detect the exact position of mutation.