Module 5: Sequence Alignments



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Various protein or DNA sequences are aligned, either pairwise or in a multiple format, to accomplish one or more of the following goals.

  • To search for a stretch or stretches of consensus sequence to the aligned components.
  • To identify and/or confirm the function of a newly sequenced gene or gene product; the alignment could also match a region within the gene or protein to a specific functional domain, eg., DNA binding region in a nucleus-bound protein.
  • To detect and measure phylogenetic or evolutionary similarities and/or variations between different species (See Module 8 for more details).
  • To obtain a rudimentary sense of the structure-function relationships that could be shared between the aligned sequences. Common secondary and tertiary structures shared between two or more polypeptides could provide clues as to the nature of such structure-function relationships.

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