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• (15 minutes) Use PRSS determine if there is significant similarity between the proteins with gi numbers: 2506213, 2493127, 4323566, 2983405, 1303679 . Choose one of these sequences and compare it to all the other ones. (The 1st row (closest to the door) will use the 1st sequence, the 2nd row the 2nd sequence, etc..) We will combine the findings from the different rows into a single table. Please enter the pseudo E-value for 10000 comparisons into the table on the whiteboard and below..

  You sequence 1:

  E-values for comparison to
  2506213:
  2493127:
  4323566:
  2983405:
  1303679:
  

• (15 minutes) Repeat a few of the pairwise comparisons using Pairwise BLAST (go here). You can paste the GI numbers directly. You have to choose blastp as the program to use. (You can force the program to report insignificant alignments by increasing the expect value).

  What do the E-values mean in case of pairwise blast? (Hint: check the output after clicking align.)
  
  
  How do these E-values compare to the ones obtained using PRSS?
  
  
• (5 minutes) You find that sequence A (gi|1303679) has a significant similarity to sequence B (gi|2506213) and sequence B has significant similarity to C (gi|2983405), but C and A are not significantly similar. Can you nevertheless conclude that A is homologous to C (two characters -sequences, or morphological characters- are homologous if they are derived from the same character existing in some ancient organism)?
  
  
  
  
• (10 minutes) Does the same reasoning hold for gi|6320016, gi|1303679, gi|2507047?
  Why might this case be different from the previous one?
  How does the output from the pairwise blast comparison help you to draw a conclusion (compare 6320016 with 1303679 and 6320016 with 2507047)?
  

 

• (10 minutes) Do a databank search of the Swissprot database with (gi|2493127). Fasta is accessible through the web at http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi. (Enter the sequence on the form, select the swissprot database as target, leave everything in the default options.)
  How many proteins show significant sequence similarity to the query sequence? (Give number of hits and the E-value cut-off you chose.)
  What type of sequences are among the matches?
  In comparing the number of actual matches (==) to the distribution fitted to these data (*) for each alignment score (given in the left column), for which value of score(s) does the number of actual hits deviate from the expectation?
  In the pairwise alignments, what is signified by the ":" and the "." ?
  

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