Bioinformatics Exercises
  B.Hands-on. Sequence Analysis I
  Writer : Seyeon Weon   Updated : 10-14   Hit : 2672   Updates 

(For those who have taken the courses and want to submit for evaluation, please read the instructions linked on the table of contents page.)

Using the sequences from B.Hands-on. Sequence Retrieval and Manipulation, do the following:

  1. BLAST:

    Visit NCBI BLAST site, and do the following:
    1. Run PSI-BLAST using the sequence of your choice from project 1.
    2. Describe the result briefly. Do not submit the result itself.
    3. 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.

  2. Multiple Alignment:

    With the sequences from problem 1, do the following:
    1. Install ClustalW and do multiple alignment with the sequences.
    2. Submit the postscript output of the multiple alignment.

  3. Motif:

    Visit expasy site and do the following with one sequence from above, and submit the summary of the results:
    1. Physical properties of your protein.
    2. Clues of some structural characteristics of your protein.
    3. Motifs in your protein.

  4. Phylogenetic Tree

    Using the same sequences as in problem 2, do the following:
    1. Using NJplot and draw phylogenetic tree using the tree data from problem 2. Submit the tree drawing in postscript file.
    2. 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.)

  5. Homology Modeling and Summarization:

    Using the sequence in problem 3, do the following:
    1. For extra points, visit SWISS-MODEL and do homology modeling for your protein.
    2. Summarize everything that you have found out so far for your protein.