BIO306 Genetics: Lab#1 Assignment (5 points)

RETRIEVING YOUR FRUIT FLY GENE SEQUENCE
Visit the following link:
http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene

Be sure that the pull-down menu next to “Search” is on “Gene”.

Then type in “Drosophila *****” where ***** is the name of the gene that you are working with and hit “Go”.

NOTE: If you have the Bar mutation, type in BarH1.

You will retrieve the most relevant links that match your query.

Scroll through the list and look for the one that has the same symbol as your gene mutation (as written on your fly vial or found in the fly manual). Be sure that this hit also has Drosophila melanogaster listed.

For example, this is NOT correct for the white gene because it has the wrong gene symbol:

and this is not correct because it isn’t from Drosophila melanogaster (it is from Homo sapiens and it has the wrong gene symbol):

Once you have found the correct gene and organism, click on the blue gene symbol and you will be sent to another page containing information about your gene. Scroll to the bottom and look for a region of the page that resembles the following:

Go to the section entitled “NCBI Reference Sequences (RefSeq)” and click on the first accession number (an “NM” number) that immediately follows the words “mRNA and Protein(s)” (highlighted in red in the example above). This will take you to yet another page that contains information about the gene sequence, including publications regarding the original sequencers of the gene, other features of the gene that we will not deal with at this time, possibly a protein translation of the gene using single letter amino acid abbreviations (in capital letters), and a nucleic acid sequence in small letters (acgt). Highlight the entire nucleic acid sequence, and then copy it. You will be pasting the sequence into your Biology Workbench account.

Also, paste your sequence into a Microsoft Word file and email this file to your lab instructor.

DEPOSITING YOUR GENE SEQUENCE INTO BIOLOGY WORKBENCH
You will be shown how to open a Biology Workbench (BW) account during lab. If you did not attend the first lab, you will need to meet with your lab instructor to learn how to open an account. It will take about five minutes. (Alternatively, you can try to figure it out yourself).

Visit the BW link:
http://workbench.sdsc.edu
Click on the large Enter Biology Workbench 3.2 link:

Type in your user name and password:

Click on Session Tools:

Click on Start New Session and then click Run:

When prompted for a Session description, name it something relevant. Then click on Start New Session.

From now on, when you enter BW, all you need to do is select this session, hit Resume Session, and everything that you have done will still remain in that session folder. For now, you only need to select Nucleic Tools:

You will be told that your folder is Empty. To add the sequence that you have copied from NCBI, click Add New Nucleic Sequence and then Run:

Label the sequence something descriptive such as the name of the mutation. Then place your cursor into the field labeled Sequence and paste the nucleic acid sequence from the gene into that field:

Click on the Save button (below the field of sequence that you have just entered):

The file should show up with the name that you gave it:

If you want to check the sequence, select the box to the left of the file, then scroll down a bit to select View Nucleic Sequence and then Run. A new window will open up, showing the sequence that you entered.

NOTE: If you have two different mutations, repeat this process to find the second gene and deposit it into Biology Workbench as well.

That’s it! We will be using these sequences later in the semester. Don’t forget to email this file to your lab instructor (along with the name of your fly gene(s)) as a Microsoft Word file for grading!! (NOTE: It HAS to be Microsoft Word and a *.doc file; we cannot always read other types of word processing files with our computers and will return it to you ungraded).