Introduction
Pairwise alignment (of nucleotide or protein sequences) means determination of mutual similarity between two sequences. This may be random or a consequence of evolutionary relationship (homology) between them. Two approaches are applied:- Global alignment (Needleman-Wunsch algorithm) – compares whole sequences
- Local alignment (Smith-Waterman algorithm) – compares individual segments within sequences
Task no. 1 - Using databases of the SRS system, try to find nucleotide and amino acid sequences for an enzyme with EC 2.7.1.40 number from these two organisms: Plasmodium falciparum and Mycobacterium tuberculosis.
- Using algorithms of global and local alignment (programs NeedleN and WaterN) compare DNA sequences.
- Using algorithms of global and local alignment (programs NeedleP a WaterP) compare protein sequences.
From obtained results of all four analyses, try to answer following questions:
- What are the values of identity, similarity and score from each individual analysis?
- How and why do results of global alignment differ from results of local alignment?
- How do results of DNA alignment differ from result of protein alignment? Try to decide, which of these two approaches is better in this case.
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