Instructions for Retrieving Gene Sequence and Performing BLASTN Analysis
RETRIEVING YOUR FRUIT FLY GENE SEQUENCE FROM WORKBENCH
Visit the Workbench link:
Click
on the large Enter Biology Workbench 3.2 link:
Type
in your user name and password:
Click on Session Tools:
Select the Session you opened the last time you visited Workbench for this class (e.g., you may have named it "My Fly Mutation"), click Resume Session, and then click Run:
Click on Nucleic Tools:
Select the file containing your gene sequence, then scroll down a bit to select View Nucleic Sequence and then Run:
A new window will open up, showing the sequence that you previously entered. Highlight this entire sequence and copy it.
You
are now going to perform a BLAST search using this sequence and gather
information from the search results that you will turn in to your lab instructor
during the next lab.
PERFORMING A BLAST SEARCH ON YOUR FLY DNA SEQUENCE
Go to the BLAST link:
You will do a standard nucleotide-nucleotide search (BLASTN). Paste the fly gene sequence that you copied from Workbench into the box and be sure that you are searching the "Others (nr etc.)" database (default is set at human for some stupid reason). You will need to select “More dissimilar sequences (discontiguous megablast)” in the “Program Selection” box and then click the word "BLAST".
The first screen that loads is just to let you know that you will be waiting for the program to finish the search.
(Sometimes the wait
can be several minutes so be patient).
The
final reload page will contain the results of the BLASTN search. The page has 3
sections. The first section is a graphic showing locations of similarity between
your sequence (the query sequence) and some of the similar sequences that were
identified by the program. The second section is a table of sequences similar to
your query sequence with numerical scores (E values). The third section shows
the actual alignments of your query sequence with each of the matching
sequences.