Tips For Creating Organism Specific FASTA Databases From The NCBI Nucleotide or Protein Sequence Repositories

Note: We have had trouble recently (12/2007) performing this procedure using Microsoft's internet explorer. This download procedure still works with the Firefox, http://www.mozilla.com/, browser.

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From The NCBI Home page http://www.ncbi.nlm.nih.gov/ select taxonomy and press the "Go" button, see Figure 1.

Figure 1.

You could have entered your organism of interest on the home page, however you would have missed the main taxonomy page, see Figure 2. Pretty cool, huh! You might be able to pick your organism from this common list, if not then enter it in the "for" dialog box, and press "Go", see Figure 3.

Figure 2.

Lets try entering "Pilobolus umbonatus" in the "for" box and pressing go. The result is shown in Figure 3 below. Click on the Pilobolus link to get to Figure 4.

Figure 3.

Notice the Entrez records listing in Figure 4. Wow, there are only 8 nucleotide sequences for this beast! Click on the 8 link, see the result in Figure 5.

Figure 4.

Figure 5.

Select FASTA from the display pull down menu, and in the send to box select "file". Save the file to a folder on your computer. You may only see 20 entries on the page below, however when you save to the FASTA file it will save as many as are found in the query.

Figure 6.

Figure 6. shows what the FASTA file will look like. It is basically a text file that can be searched by most of the MS sequence database search utilities.

Thanks to NCBI, now you can create accurate, and specific subset databases that you can search with mass spectrometry data. This is especially important when searching nucleotide databases since they can be very large.

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