This web page was produced as an assignment for Gen677, an undergraduate course at UW-Madison Spring 2009
ClustalW Protein Sequence Alignment
Shown above is a portion of an alignment of the protein sequences of dog, cow, chicken, mouse, human, and rat species in that order using ClustalW. Because ClustalW limits you to amino acid sequences of 2,000 amino acids in length, I was only able to align the first 2,000 amino acids of each sequence. Asterisks below a column indicated that all of the amino acids are the same. Click on the alignment above to see the entire alignment.
Another view of the ClustalW protein sequence alignment. This option appeals more to the visual learners.
T-Coffee Alignment
Above is the same alignment done in T-Coffee as opposed to ClustalW. Click the picture for the full alignment.
| clustalw_allignment.txt | |
| File Size: | 19 kb |
| File Type: | txt |
| t-coffee_alignment.txt | |
| File Size: | 20 kb |
| File Type: | txt |
References
Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed) *: joint first authors
Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressivemultiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, Nov 11;22(22):4673-80. (PubMed)
Notredame C., Higgins DG., Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000, Sep 8;302(1):205-17. (PubMed)
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Last Updated 5/13/09
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