In the report JUST give the answers - DO NOT print out the questions and write the answers in.
READ THROUGH THE WHOLE ASSIGNMENT BEFORE YOU START. It will help you understand the purpose of the questions!!!!
Add your name and e-mail address on top of the page!!!
This assignment will deal with the various ways you can change parameters to fine tune a database search.
Our target gene is Lip1, a single-pass transmembrane protein that is required for de novo ceramide (sphingolipid) synthesis in yeast. According to the local campus bioinformatics expert, the gene is limited to a very specific branch of fungi. As the other genes involved in ceramide synthesis are highly conserved in almost all eukaryotes, you find this strange. Your job is to see if what was reported is correct, and to try to find the gene in other species (particularly mammals) as well.
Enter the NCBI web site (this will open a new window): http://www.ncbi.nlm.nih.gov/ and get the protein. The accesion number is: NP_014027
Go to the protein blast page: Blast at NCBI
and run a search with most of the default parameters. Go to the bottom of the page and click on the 'Algorithm parameters' blue bar. Change the Expect threshold (E value) to 10, to allow for more distant sequences.
Now that we have a baseline, we'll start to change parameters (click "Edit and Resubmit" from the top of the page, do not go back, it doesn't work in all browsers. Be sure to change the title of the search so that you can keep track of what you've done. This can be done in the 'Job Title' line under the box where you paste the sequence). The first thing we'll do is change the word size to 2 keeping the E value at 10, and run the blast again.
Now we are going to change databases. Click "Edit and Resubmit" again. Change the wordsize back to 6, leave the E value at 10, and the database to swissprot.
Now we'll see what changing the matrix will do to the search. Click "Edit and Resubmit" again. Change the database back to nr, and change the matrix to PAM250 (wordsize should be 6, E value 10).
One last time, we'll change the matrix again, this time to PAM30.
To summarize: