Clustal Omega protein alignment
We are going to use the clustal omega program to analyze some homologous proteins to the human frataxin in mammals.
You can use clustal omega in the ebi server. There are also on-line servers that create clustalw alignments and you can read its
Create an alignment check the result. Is there any problem?
What would happen if we remove the most dissimilar sequences
Redo the analysis only with the closest mammals and compare the result with the previous one.
What would happen with more dissimilar sequences
Try to do the alignment with more different sequences.
Compare the result with the one given by T-Coffee
Once you have the result you can use the TCS tool in the same server to get an idea of which sites are reliable which are not.
Compare the result with the domain stored in NCBI for the frataxin.
Is this domain similar to any of our alignments?
DNA sequence alignment
We can also align DNA sequences. This is useful to do phylogenetic analysis and to look for mutations in the sequences. We are going to look for the SNPs in the CT099 gene of Lycopersicum pimpinellifolium. Align them using MAFFT.
Take a look at the guide tree. Is this a reliable phylogenetic tree?