Name: Gabriela Gaytan
Open your sequence file, and copy and paste all of the text into the “
” text box on the BLAST page.
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.
NCBI will 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 the page.
When the results page appears, scroll down to the “
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.
Run your Blast 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 DNA