1. Homework Assignments due next session 1.Find a entry of interest in OMIM ( http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM ) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM 2.Find a Gene associated with that entry 1.Click on the “links” link on the right and choose “Gene”

2. Homework 3.The Gene page has gathered scads of information about this one gene. Find homologs in other species. From this page again choose “links” and go to Homologene

3. Homework 1.Gather the protein sequences for each homologous gene (or 5 of them if there are more than that). 1.Click “DownLoad” in the homologene listing 2.Download everything with the default settings.

4. Homework You will get a text file in “Fasta” format. Save it somewhere convenient.

5. Homework Go to the Clustal server at http://searchlauncher.bcm.tmc.edu/multi-align/multi- align.htmlhttp://searchlauncher.bcm.tmc.edu/multi-align/multi- align.html Paste your complete Fasta file contents into the input box and click submit. This takes awhile, so be patient. You will get output that looks something like this.

6. Homework At the bottom of the alignment file is the same results in “Fasta” format. Copy the complete Fasta results and paste it into the input box at a BoxShade server (http://bioweb.pasteur.fr/seqanal/interfaces/boxshade.html)

7. Homework Depending on the parameters chosen for BoxShade, you will see something like this. Regions which are the same in all species are likely involved in function in some way.

8. Homework After all that work, your boss comes to you ands says that sequence comparison is obsolete! He wants you do structural alignments of these proteins. Figure out what a structural alignment is, find two different tools to find conserved 3D structures and choose which one you would use for this. Describe why this tool is preferable to the other. NOTE: You do not need to actually do any structural alignments. Just find out how you would go about doing on if you had to.