MotivationThe biological motivation for studying this problem comes from the fact that high degree of similarity of bimolecular sequences usually implies significant structural and functional similarity.Generally, such comparisons involves aligning sectionsof the two sequences in a way that exposes similarities between them.
Motivation•The sequence similarity is also relevant in the context of understanding the molecular basis of evolution. •It is well known that the closely related organisms have high similarity between their genomes. •Study of conserved sequences among the organisms reveal past speciation and the structure of ancestral family trees and the role of mutation in the evolution of these trees. •Studying similarities within the individual organisms in a species might also reveal whether certain individuals are prone to inherited diseases. •There are many other examples from biology that illustrates the use of sequence similarity.
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Alignment Example•Consider the alignmentbetween two protein sequences vand w(monkey sematotropin and its precursor in rainbow trout) .•v: L E P V Q F L R S V F A N S L -V Y G T S Y S•w: E Y P S Q T L - - I IS N S L M V - R N A - N•The aligned pairs of symbols are written one above the other. Symbols in one sequence that is not aligned with symbols in the other are written opposing the symbol „-‟. For example, „RS‟ in sequence vconstitutes a gapof two symbols. To maximize similarity of two sequences, we want to find alignments that have few gaps and align symbols that are identical or whose functions are highly similar.