Visit NCBI BLAST site, and do the following:
- Run PSI-BLAST using the sequence of your choice from project 1.
- Describe the result briefly. Do not submit the result itself.
- Obtain the sequences for which you want to do multiple alignment. Since you will not be using a supercomputer, do not choose too many sequences.
- Multiple Alignment:
With the sequences from problem 1, do the following:
- Install ClustalW and do multiple alignment with the sequences.
- Submit the postscript output of the multiple alignment.
Visit expasy site and do the following with one sequence from above, and submit the summary of the results:
- Physical properties of your protein.
- Clues of some structural characteristics of your protein.
- Motifs in your protein.
- Phylogenetic Tree
Using the same sequences as in problem 2, do the following:
- Using NJplot and draw phylogenetic tree using the tree data from problem 2. Submit the tree drawing in postscript file.
- For extra points, visit PHYLIP and install the package locally. Do tree construction and submit the resulting tree. (There are a few web servers, but I don't think that it is wise to use them for our purpose.)
- Homology Modeling and Summarization:
Using the sequence in problem 3, do the following:
- For extra points, visit SWISS-MODEL and do homology modeling for your protein.
- Summarize everything that you have found out so far for your protein.