Solved 3.Run a standard protein-protein BLAST of the globin

3.Run a standard protein-protein BLAST of the globin sequence GLB5_PETMA against the SWISSPROT database; write down the number of hits and the E value of the least significant hit. Now run PSI-Blast with the same sequence; write down the number of hits and E value of the least significant hit for each of the first three iterations. Using these results as an example, explain the advantages of PSI-Blast over standard protein-protein BLAST. Does this method have any drawbacks?

4.Go to prosite.expasy.org/prosuser.html and scroll down to the short example profile and its weighting matrix. Score the following sequence against the matrix:

WVAASQCALD

Calculate the ‘order of complexity’ of aligning this group of 7 sequences using a dynamics programming method, assuming that gaps are allowed. Why are these methods used only very rarely in multiple alignments?

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