Because of the skipped class on  MLK day, I am going to give some extra homework.

This is a hands-on experience, and will involve a little bit of groping around and frustration,
so work together with a friend, and limit it to a reasonable amount of time. We will go over it
in class next time.

The idea is to give you some experience in what you might do in the real world, where you often need to
figure something out that is a little vague and there is no one to tell you what to do. also, you
can evaluate the benefits and limitations of an important genomics resource.

this is probably a lot more than anyone can complete, but try it out and we will spend most of the
next lesson going over it in class. you will appreciate it more in class if you try it yourself
first. 

1. Find the names of a few human genes (hint - go to NCBI site at http://www.ncbi.nlm.nih.gov and
click on pubmed. do a search on  some disease and a few gene names should pop up)

2. Do a search for the sequences of these genes using BLAST on the NCBI site.

3. Go to the UCSC site (use a search engine and look for BLAT and ucsc) and submit one of your sequences
to BLAT (copy and paste)

4. open another browser window and repeat the same BLAT query

5. click on detail in one window and viewer (I think) in the other window

6. in the genome viewer window, click on  bases within the zoom options bar

7. here is the hard part: using the info the details window and reading the documentation under help,
try to navigate to the left hand end of the gene (the trick is to mentally go back and forth between 
the coordinate systems for the query sequence and for the genomic sequence)

8. see if you can find some of the signals that are in the book chapter, like initiation methionine (ATG)
or splice junction signals.

9. there is a 50/50 chance that the gene you selected will be the reverse complement (look this up if you
do not know what it means). for instance, ATG at the left end will be TAC at the right end.

10. if you are really lucky, you can check out a few amino acids in the sequence using the table in the textbook that shows the genetic code.