PartI.Seq.Align - Comparing biological sequences: sequence...

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Comparing biological sequences : sequence alignment
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Motivation The 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.
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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 alignment between two protein sequences v and 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 I S 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 v constitutes a gap of 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.
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Alignment Example The dual perspective is to consider sequence v evolve into sequence w and we seek alignments with minimum distance or intuitively minimum number of evolutionary operations that converts v to w . In this perspective, an aligned symbol of w is substituted for its corresponding symbol in v , an unaligned symbol (that is, aligned with „-‟ symbol) of v is deleted and an unaligned symbol of w is inserted . In the example, symbol „E‟ of w is substituted for „L‟ of v , and the symbols „RS‟ in v constitute a deletion gap . Similarly, the symbol „M‟ in w constitutes an insertion gap of one symbol. The symbol „-‟ is also referred to as an „indel ‟ standing for either insertion or deletion.
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DNA Sequence Comparison: First Success Story Finding sequence similarities with genes of known function is a common approach to infer a newly sequenced gene’s function In 1984 Russell Doolittle and colleagues found similarities between cancer-causing oncogene ( v- sys in Simian Sarcoma Virus) and normal growth factor (PDGF) gene
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Other Examples The first successful sequencing of the genome of a living organism in 1995 of the bacterium Haemophilus influenza rd (Fleishmann et al, 1995). After that, researchers identified 1743 sites as prospective gene sites.
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This note was uploaded on 06/12/2011 for the course CAP 5510 taught by Professor Staff during the Spring '08 term at University of Central Florida.

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PartI.Seq.Align - Comparing biological sequences: sequence...

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