<p> Genbank Assignment</p><p>You are called to the scene of a gruesome murder in the primate house at the local zoo. An apprentice keeper has been strangled to death. The victim and your friend, the head primate keeper, were the only people in the locked building at the time of the murder. According to the policeman on the scene, your friend is the prime suspect. You find blood under the victim's fingernails and extract DNA from the blood. Though little intact DNA is present, you do get the following DNA sequence. gaaaaaaaat cgagtaagag accactgtgg cagtgattgc acagaactgg aaaacactgt</p><p>(copy and paste the above sequence into the BLAST search box)</p><p>Who is the killer?</p><p>Can this sequence data be used to determine the killer's identity?</p><p>Use the National Center for Biotechnology Information BLAST server to solve this mystery. </p><p>The NCBI site is a repository for various DNA and protein sequences and a lot of other information. There are zillions (well, actually something over 100 billion, as of 2005) of bases of DNA information in there. Thousands of organisms are represented. Many have ALL of their DNA sequence (their entire genome) in the database. Most have varying amounts. This is a fantastic resource for researchers. </p><p>You are going to get a crack at using the GENBANK database. Because the site has all kinds of links and it takes some familiarity with all this stuff to navigate, the instructions will send you straight to the appropriate search engine and even set the defaults for you (all in the magic of a single URL!). Your job will be to submit the sequence, run the search and interpret the results.</p><p>Here's what you do:</p><p>1. Go to the class web site.</p><p>2. Follow the link for “Class Handouts”.</p><p>3. Find this handout and open this document in Word.</p><p>4. Highlight and copy the nucleotide sequence given above. Close the Word document. 5. Use the back button on your browser to return to the Index page of the class web site.</p><p>6. Click on the link for “Genbank Assignment”. The NCBI BLAST web page will open in a new browser window.</p><p>7. Paste the nucleotide sequence into the Enter Query Sequence box.</p><p>8. Under the Choose Search Set database option, select the Others (nr etc.): button.</p><p>9. Hit the big blue BLAST button at the bottom of the page.</p><p>10. Wait. It may take a few seconds for the results to appear.</p><p>11. Your results appear. Identify the killer.</p><p>There is a lot of information on this screen. Scroll down past the distribution graphic (the box with colored lines), and scroll past the list of sequences. They're sorted in order from the best match down. Further down the page you will see the Alignments.</p><p>Alignments show exactly how your sequence lined up against sequences in the database. Both sequences are shown lined up against each other. There is a Score, which is a measure of how well they matched, and a line that says "Identities =", which tells how many of the total nucleotides were the same, and then gives a percent identity in parentheses. </p><p>To determine the identity of the killer, you need to find a perfect 100% match [Identities = 60/60 (100%)] Try looking at the top scoring hit (at the top of the list) -- just click on the score for that hit and it will take you down the page to more detailed information.</p>