BLASTing your unknown sequence

One of the easiest ways to identify the origin of the sequence is to compare it to Genbank.

Right click on the "Consensus bear bile" sequence and click the BLAST button on the toolbar. Set Database to "Nucleotide collection (nr/nt)" and Program to "blastn". Leave the other settings at their defaults. Next click the Search button and your sequence will be compared against GenBank. Be patient, this may take some time. Look at the best matches from the BLAST search. There should be a few GenBank records that are exact (100%) matches for the consensus sequence (these can change as new sequences are deposited into GenBank).

Select the GenBank entry with the accession EF076773. Download the full sequence. This is a whole mitochondrial genome for Ursus thibetanus formosanus. In the sequence view, you can locate your BLAST hit by turning annotations on and selecting "BLAST Hit" from the list of available annotations. You will notice that in this exercise we have amplified a piece of DNA from the 5' end of the CytB gene (turn on CDS annotations if necessary to see this).

Question 3: From information in the GenBank file, what is the common name of the closest GenBank match to the sequence we have obtained from the bear bile crystals?
> 


Question 4: The WikiPedia link for Ursus thibetanus formosanus can be found here. From the information on this page - what is the conservation status of this subspecies?
> 


Exercise 4: Build a phylogenetic tree