This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009
T-coffee DNA sequence alignment
This file is a DNA sequence alignment using T-Coffee (2) of the Homo sapiens SIRT6 gene against Mus musculus, Danio rerio, Gallus gallus, Rattus norvegicus, Pan troglodytes, Drosophila melanogaster. I did this alignment to see how well the coresponding base pairs for each organism would match up.
| get_result.pdf | |
| File Size: | 198 kb |
| File Type: | |
ClustalW2 DNA alignment
This is another DNA sequence alignment of Homo sapiens SIRT6 against Mus musculus, Danio rerio, Gallus gallus, Rattus norvegicus, Pan troglodytes, and Drosophila melangoaster but this time I used ClustalW2 (1). This aditional aligment was done to see if I would obtain simular results of sequence aligment as the T-coffee (2) alignment.
| dna_seq.bmp | |
| File Size: | 1155 kb |
| File Type: | bmp |
Results
The DNA base pair alignement seemed to follow along pretity much what my phylogenetic tree showed me. And that is that human and Pan trogldytes have score of 99 (meaning a very similar base composition). While rat and mouse had a very high base pair similarity also. It is interesting to note that gallus had scores very similiar for all species which I would have thought it would have been a little more similar to human or mouse and less simliar to drosophila.
References
1. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007). ClustalW and ClustalX version 2. Bioinformatics, 23(21): 2947-2948. doi:10.1093/bioinformatics/btm404.
2. Notredame, E., Higgins, D.G., and Heringa, J. (2000). T-Coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1):205-217. doi:10.1006/jmbi.2000.4042.
Mark Devries
Email [email protected]
last updated 1/22/09
http://www.gen677.weebly.com
