Pairwise Sequence Alignment

1. Download the protein sequences hypoxanthine phosphoribosyl transferase (HPRT) for mouse and E. coli in FASTA format from the NCBI database.
2. Perform a dot matrix alignment using the program Dothelix
   http://www.genebee.msu.su/services/dhm/advanced.html.
3. Perform pairwise alignment the program ClustalW2
   http://www.ebi.ac.uk/Tools/clustalw2/
4. Perform a local alignment using the program LALIGN
   http://www.ch.embnet.org/software/LALIGN_form.html.
5. Perform a global alignment using the program LALIGN (Compare the global and local alignment).
6. Change the gap penalty from "-14/-4" to "-4/-1" and run a local alignment. (Compare with previous results).
7. Do a pairwise alignment using BLAST (bl2seq program located under section "Specialized BLAST" on the NCBI BLAST homepage).
   (Compare with previous results).
8. Use the exhaustive alignment program SSEARCH
   http://pir.georgetown.edu/pirwww/search/pairwise.shtml (Compare with previous results).
9. Finally check with the program PRSS
   http://fasta.bioch.virginia.edu/fasta_www2/fasta_www.cgi?rm=shuffle if there is any statistically significant similarity between the two sequences. (Study the output and try to find the critical statistical parameters).