Pairwise alignment

In this this mini-exercise you will use the pairwise alignment server at The European Bioinformatics Institute (EMBL-EBI, which is part of the European Molecular Biology Laboratory, EMBL):

1. Open the pairwise alignment page at EBI: http://www.ebi.ac.uk/Tools/psa/.

2. Select global alignment ("EMBOSS Needle") of protein sequences.

3. On the EMBOSS Needle page: Copy and paste the two sequences below into the two windows (these are the sequences you have investigated in a handout exercise previously):

   >seq1
   ALWGKVHWGEYV
   
   >seq2
   AAWGKVGWHAGGYV
   

4. Set the substitution matrix, gap opening penalty, and gap extension penalty to the same values that you used in the handout exercise (click the "More options" button and use the dropdown menus to set the desired parameters).

5. Start the program (by clicking "Submit") and compare the output to the result in the handout exercise: What is the score of the best possible alignment? Is it better than the two alignments we looked at?

6. Below is a set of glycophorins from Man and Horse (glycophorins are proteins that are present in the membrane of red blood cells):

   >GLPA_HUMAN 150  P02724 GLYCOPHORIN A PRECURSOR 
   MYGKIIFVLLLSAIVSISASSTTGVAMHTSTSSSVTKSYISSQTNDTHKRDTYAATPRAHEVSEISVRTVYPPEEETGER
   VQLAHHFSEPEITLIIFGVMAGVIGTILLISYGIRRLIKKSPSDVKPLPSPDTDVPLSSVEIENPETSDQ
   
   >GLP_HORSE 120  P02726 GLYCOPHORIN HA. - EQUUS CABALLUS (HORSE).
   QTIATGSPPIAGTSDLSTITSAATPTFTTEQDGREQGDGLQLAHDFSQPVITVIILGVMAGIIGIILLLAYVSRRLRKRP
   PADVPPPASTVPSADAPPPVSEDDETSLTSVETDYPGDSQ
   

7. Open two browser windows on the EBI alignment server. In one window align the glycophorin sequences using global alignment ("needle"). In the other window align the sequences using local alignment ("water"). Note the difference.

8. Again use your two open browser windows on the EBI alignment server. In one window align the glycophorin sequences using local alignment ("water"), with the following settings:

   subsitution matrix: BLOSUM62
   gap-opening: 10
   gap-extension: 0.5
   

   In the other window align the same sequences using local, with the following settings:

   subsitution matrix: BLOSUM62
   gap-opening: 100
   gap-extension: 10
   

   Compare the resulting alignments.