Snow Day!

I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it.

Even the kids aren't looking too happy about it, though. By this time of the school year, they've caught on that every snowday has a price. And, they will pay that price IN JUNE. Already the last day of school has been postponed until the 25th of June.

Who knows? The kids might even be in school until July. At our house, snow day payback days are no longer topics we're allowed to joke about.

Just in case, you're a bioinformatics student who happened to check in, and you haven't gotten set up on Blackboard, I do have a couple of fun assignments for you to try at home.

This question is modified from an activity by Peter Cooper at the NCBI. All I can say, is well, if there's something interesting in GenBank, Peter is bound to know about it.

Question 2 (from the handout): Is the answer with the best significant E value, or bit Score, always the right answer?

Instructions:
1. Go to the NCBI page for doing a blastn search. (link)
2. Paste U41319 in the search box. (U41319 is the accession number for the sequence).
3. Choose Others (nr) as the database.
4. Click the BLAST button.

And, think about the results. What do think this sequence is?

Question 4 (from the handout): Use blastn to see where PCR primers are hybridizing to a target sequence.

Instructions:
1. Go to the NCBI BLAST selection page and choose "Search for short, nearly exact matches."
2. The primer sequences are:

Forward primer: 5'-GTTCGGGGAGATGGAGTGCT-3'
Reverse primer: 5'-CGTTGCGGGACAGATTGATT -3'

3. Paste the forward primer sequence in the search box (just use the letters).
4. Then type about 20 N's, like this NNNNNNN, etc.
5. Then, enter the reverse complement of the reverse primer sequence. (remember it will be the 5' to 3' sequence for the strand that's complementary to the reverse primer).

6. And, last, you guessed it, Click the BLAST button.

What database sequences do those primers detect?

If you want to post your answers here that's great, but I won't answer anything until next Weds or Thurs., after class.