dear Mudler,
The choice of method for phylogenetic study will be based on your objective
First make it clear about your objective. then i can help you
The particular protein is protein S. Protein S is a vitamin K-dependent glycoprotein that functions as a non-enzymatic cofactor for protein C in the proteolytic degradation of activated factors Va and VIIIa. Through this mechanism, and others, the thrombingeneration is regulated. Protein S deficiency is a wellknown risk factor for venous thrombosis and possibly also for arterial thrombosis. To exame the mechanism by which protein S deficiency predisposes to thrombosis as well as the molecular mechanism underneath, could help in understanding the biological importance. Therefore, I would like to analyse the molecular evolution of protein S and consequently unravel the biological properties of protein S during this process.
Dear Dr. Mudler
kindly visit the following URL
http://jb.asm.org/content/179/9/2793.full.pdf
this may help you
Hello René,
I suggestie that you run a blastp search of your S protein amino acid sequence against the swissprot database to collect all homologous protein sequences. If that search does not give you enough sequences of interest you could take the Uniprot database. Align the sequences of your choice using the program ClustalX with default settings and save the alignment. now run from inside ClustalX the tree program with correction for multiple substitution and with exclusion of gaps. The resulting tree file with suffix .ph can now be imported in a tree presentation program such as Treefig or NJPlot. This will give you a first idea of the characteristics of the evolution of your protein. At a later stage the sequence databse can be adapted and more sophisticated analyses can be carried out. In the case you would be hesitant to carry out these analyses all alone or you should have difficulties to find and instaal the necessary programs, we can do this together.
René,
I suggest that you read my chapter (attached) on the subject. It contains a complete section with practical exercises as well. If you have any questions you may contact me by mail at [email protected]
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