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1. Assume that you are interested in heat shock proteins. You happen to come across a particular heat shock gene found in all Archaebacteria of the genus Methanosarcina. Using the Blast data bank search tools at the NCBI, you want to assess to which other heat shock molecule this genes is similar to. This sequence can be found here. Copy the sequence in FASTA format, go to the NCBI BLAST page and do a nucleotide BLAST search using Blastn of the nr database. What are the results of your BLAST search? How many significant hits did you get? What can you say about the quality of hits from sequences belonging to other genera? (Hint: look at the graphic summary.)
   
   
   
   
2. Using the same query sequence (i.e. the nucleotide sequence), do a Blast search using the translated query vs. protein database search tool (Blastx) and the translated query vs. translated database search tool (Tblastx). Do you notice any differences in results as compared when using Blastn?
   
   
   
   
3. Based on those previous Blast searches, what can you conclude on the possible origin of this particular heat shock protein found in Methanosarcina? (Hint : From what domain of life the hits are from? Archaea, Bacteria or Eukaryotes?) Rather than doing the BLAST searches yourself, what other tool offered through the NCBI could you have used?
   
   
   
   
4. Do an additional BLASTP search with gi|12585422.While waiting for the results, take notice of the conserved domain results on the format page. Inspect the graphical summary alignment on top of the blast result page.
   What might be the reason for the black area in the target sequences that correspond to the center of the query sequence? (Hint : You might want to do a litterature search about Inteins)
   
   
   
   
5. Find the E.coli K12 S14 ribosomal protein in the genbank database. Run a BLASTP search limited by the ARCHAEA query (select from the pulldown menu on the BLAST page). Do you find a significant match to this protein in any archaeal species? Why or why not? What BLAST search should you do next in order to further check for the presence of S14 in the Archaea?
   
   

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