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Computational Biochemistry for beginners
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Searching the NCBI Protein database for protein sequence information


The protein sequence of lots of organism has already being deduced, most of the known protein sequence can be accessed from the NCBI protein database. Below is a brief tutorial on how to obtain any particular protein sequence information from any particular organism.

  • Point to the browser to the NCBI home page www.pubmed.org
  • Select protein from the Search pull down menu, (See shortly below).


Pubmed home page screen shot


  • Alternatively, point your browser directly to the NCBI protein home page: http://www.ncbi.nlm.nih.gov/protein
  • Type in the protein name in the “Search” textbox, and click GO or SEARCH button
  • A summarized format of the results are displayed. Scan through the result and identify the entries that interests you. The organisms of the output sequence is indicated beside each of the summarized result. see FIG 2
  • You can limit a search by specifying the name of the organism in bracket after the protein e.g. metalloprotein [homo sapiens]

NCBI protein result page


  • Below each of the output result is the number of amino acids, (aa), the NCBI protein accession number, and the GI number.
  • The accession number uniquely identifies each entry in the NCBI protein database. You can access any particular entry in future by searching the NCBI protein database with its accession Number.
  • The default format of displaying the result is a summarized listings, you can tick on the set of sequence that interests you and then select other formats for more detail information on the protein sequence.
  • To select other formats, click the pull down menu that is labeled "display", above the results. (Mouse over FIG 2 to see a clearer image)
    result formats of NCBI protein database
  • As noted above, there are different available format that the results can be displayed in. The FASTA and the GenePept format are discussed briefly below. There is no harm if you try out the other available formats.

FASTA format.
FASTA format is a format used mostly by many sequence analytical tools and software. It lists the sequence information on the first line and then the sequence itself is listed immediately below in a capitalized single lettering form of representing amino acids.

This is the default way of displaying the entry, it contain detail information about the sequence, the reference of the work that provided the available information on the sequence, reports on the unique compositions of the sequence, the sequence itself. etc

After selecting the formats that interests you, you can download the report in a text or printer friendly format by clicking the download option.

Consult the site documentation and help for more information on using NCBI Protein database


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