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Computational Biochemistry for beginners
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Searching the NCBI Nucleotide database for Nucleotide sequence information


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

  • Point to the NCBI home page www.pubmed.org
  • Select NUCLEOTIDE from the Search pull down menu, (Fig 1.
  • Type in the protein name in the “for textbox” and click Search

Pubmed home page screen shot


  • The summarized formats of the results are displayed. Scan through the result and identify the entries that interest you. The organisms of the output sequence are indicated beside each of the summarized result.
  • You can limit a search by specifying the name of the organism in bracket after the protein e.g. metalloprotein [homo sapiens]

The result page of nucleotide database search of NCBI



  • Below each of the output result is the number of base pairs in the DNA sequence, (bp), the type of sequence (DNA, mRNA, EST, synthetic construct), the NCBI Nucleotide database accession number, and the GI number.
  • The accession number uniquely identifies each entry in the NCBI Nucleotide database. You can access any particular entry in future by searching the NCBI Nucleotide database with its accession Number.
  • The default format of displaying the result is a summarized listings, you can tick on the set of sequence(s) 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)
    Formats of nucleotide result entry; NCBI
  • As noted above, there are different available format that the results can be displayed in. The FASTA and the GENBANK 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 nucleotide bases.

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. 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 Nucleotide database


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