BLAST LAB: Probing the National Center for Biotechnology Information – Revised 2/7/2016

INSTRUCTIONS:

1. OPEN: http://digitalworldbiology.com/dwb/BLAST Work through the tutorial.

2. OPEN http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

3. Using (your choice) 1 of the 16 of the sequences on the web page: http://www.digitalworldbiology.com/BLAST/62000sequences.html , copy the nucleotide sequence into clipboard.

4. Go to the BLAST page and insert this sequence (paste) into the FASTA block. At the bottom of the page, click the BLAST button. Be patient and wait for the results.

5. Answer the questions below. REPEAT questions 2-6 for 5 more sequences (for a total of 6 sequences researched). Organizing your results into a chart may be helpful.

6. Choose ONE of your sequences to answer 7-10.

BLAST QUESTIONS

Include the source of the information along with your answer. In this case, the source will be the database or web page that provided the information.

1. What is the NCBI database? Who enters sequences into the database? Why do scientists find it useful?

2. How long was the query sequence used to search the database? Hint: This sequence is so named because you used it to ask a question (query) of the database.

3. What is the most likely identity of this sequence? What data supports this conclusion? Hint: Refer to the slide in the BLAST tutorial that discusses the E value.

4. What organism was the most likely source of the sequence? Hint: Refer to the BLAST tutorial to find an overview of the GenBank nucleotide record. If more than one organism matches, look at the E values to determine the most likely match.

5. What is the common name for this organism? Hint: Refer to the GenBank nucleotide record. It may also help to look at the Taxonomy database. The BLAST tutorial shows where to find this link.

6. What phylum contains this organism? Hint: Refer to the taxonomy database. The BLAST tutorial shows how to find the link.

7. Is this sequence expressed? How do you know? Hint: Gene expression includes the processes of transcription (making RNA) and translation (making a protein). Determine if either of these molecules is described in the sequence record.

8. What is known about factors that affect expression of your DNA sequence? Hint: The title of the submission is a good place to start. PubMed records and the Entrez Gene database are also helpful.

9. If possible, give the names of three different organisms with significant E values. If an organism is represented, then write down the name of that organism. Hint: Refer to the BLAST tutorial slide on E values for a description. 10. Use GenBank, PubMed, Gene, and UniGene records to find the possible function of the protein that's specified by your DNA sequence. Describe what's known about the role of this protein in the organism that provided the DNA.