How to Search Genbank for the Sequence of Your Favorite Protein (YFP)

This is a part of an assignment for Molecular Biology at Davidson College.

Go to <>

Click on Entrez Browser
GenBank (nucleotides and proteins), PubMed (MEDLINE),3D structures, genomes, and taxonomy databases.

Click on Nucleotides.

Change the Search Field at the top to Protein Name.

Enter the name of YFP you have gotten from RasMol.

Click on the Search button.

Click on the Retrieve button.

Search through the descriptions until you find a match with YFP that is from a genome organism.

Then go back to the top of that page and hit the "Display" button.

You want to save all of the information that comes with this new page.

Option One
Highlight the information and paste it into a WordPerfect file.

SAVE THIS FILE on your floppy and in the 24 hour storage folder.

Option Two
If Pollux will not let you highlight the file, then click under the "View" menu, select "Document Source" This will save the information in "simple text" which youcan import into WordPerfect.

While you are in WordPerfect. Select about 30-40 amino acids from YFP and copy them.

Now go back to the WWW browser.

Go back to <>

Click on BLAST
Sequence Similarity Searching Nucleotide or protein query sequences against the specified database using the BLAST suite of algorithms.

Click on Basic Blast Search (you can do either Blast or Blast 2.0. The latter does not give you as many matches but is fancier. )

On the new page, it is important that you change "program" blastp (p is for protein and n is for nucleotide).

Paste in the amino acid sequence from YFP and click on the "Submit Query" button.

You will get a list of "hits tha match your sequence. The first one should be the same sequence you submitted. Below that will be other simirlar sequences. Note that some names of species are given.

Click on the blue text to the left and you will be given a new page of information from this sequence.

Down at the bottom, you can save the report in a Macintosh Text format.

Name the file and save it in the 24 hour storage and your floppy disk.

Repeat this until you have sequence from the genome organisms or at least 5 diverse species if you cannot find all 5 of the genome organisms listed.

Plan B in case the WWW is too slow or the NCBI Server is down:

If you cannot get the web search to work, you can do the email search of Genbank.

Either way will work. With the email search, you will not have to wait as long for the graphics to come up like you do on the web. Plus, you can have the searches done and return with results to your email which you can check later. This search usually only takes less than 5 minutes. If you do this search after 9-5 pm, it goes even faster.

How to find YFP for viewing by RasMol.

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