Under the “Database” portion of the page, pull down the menu and select “
Make sure the “show results in a new window” is selected.
Click the “BLAST” button on the lower left side to start the search.
return a page telling you the search is in progress.
The search may take a few
minutes depending on server load—Do not keep submitting or refreshing
When the results page appears, scroll down to the “
first result likely represents your unknown sequence.
The top hit is most likely
the sequence from your organism.
Record the genus and species in the data
sheet below. Click on the description link for the first entry.
Observe the “
” section for your sequence.
Record the score, expect
value, and identity score in the Lab Activity 2 Datasheet below.
As you observe
the alignment, note that dashes between the query (your unknown) and the
subject (sbjct) indicate identity—a perfect match between the two sequences.
Are there any regions of your sequence that don’t have dashes?
Click on the “
” at the top of the entry.
Answer the questions for this
section on your lab data sheet.
10.Run your BLASTn search again (start at #4) using the sequence given to you,
but this time,
only use the first line of your DNA sequence as your query
Did your results change?
Answer the questions on your data sheet.
Visualizing DNA using MEGA software.
MEGA is a program preferred by many
phylogeneticists because of its simple and elegant interface for visualizing and aligning