Human NRCAM alignments Homology Phylogeny Motifs
T-COFFEE alignment
| tcoffee.pdf | |
| File Size: | 133 kb |
| File Type: | |
ClustalW alignment
| clustalw.pdf | |
| File Size: | 75 kb |
| File Type: | |
Phylogeny.fr Tree Muscle alignment
Analysis
ClustalW and T-COFFEE were used to create alignment of the following NRCAM homologs: Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, Gallus gallus, Bos taurus. These programs worked nicely together as they both used FASTA gene sequence formats to input data, and returned outputs that were organized in slightly different ways. ClustalW annotated the alignments using symbols which were defined in a key, whereas T-COFFEE returned results in a color-coordinated fashion making it very easy to fine regions of high and low homology between sequences. The two programs matched the sequences very similarly, therefore indicating that the gene is fairly well-conserved across a variety of species. The terminal residues for all of the species ad nearly 100% homology; most of the deviation occered in the middle of the sequences.
Phylogeny.fr "One Click" was used to generate the phylogenetic tree above using the Muscle alignment. The tree shows human isoform A and the chimpanzee homolog to be most closely related, with mouse and rat homologs related closely with both humans and chimpanzees. The other mammal, the cow, is more closely related to the other mammals than the chicken which we might expect. The tree agrees with the results of the alignment scores that resulted from multi-sequence alignments [1,2,3,4,5,6]. ClustalW and T-COFFEE both returned phylogenetic trees which are not shown, but will be added to the site with some of the protein data.
2. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high thoughput. Nucleic Acids Res. 2004, Mar 19;32(5): 1792-7. (PubMed)
3. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 200, Apr;17(4): 540-52. (PubMed)
4. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, Oct;52(5):696-704. (PubMed)
5. Anisimova M., Gascuel O. Approximate likelihood ratio test for branches: A fast, accurate and powerful alternative. Syst BIol. 2006, Aug;55(4):539-52. (PubMed)
6. Chevenet F., Brun C., Banlus AL., Jacq B., Chisten R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics. 2006, Oct 10;7:439. (PubMed)
