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Introduction to NCBI Bioinformatics Resources: BLASTN Nucleotide Sequence Search

A concise introduction to the various bioinformatic data available from NCBI.

BLASTN Nucleotide Search

BLASTN Example

This illustration demonstrates how to use BLASTN to search starting with a nucleotide sequence.

You can start from the NCBI BLAST home page:

Or, you can start from a Nucleotide record.  In this case, we start from the RefSeq mRNA link within the LCT Gene record:

Click on the NM_002290.2 record ID in order to display the Nucleotide record:

To search BLASTN using the mRNA RefSeq:


Or, from the Nucleotide record, find the base pair (bp) sequence:

Click on the CDS link to highlight the base sequence:

Grab the sequence and then cut&paste into the BLASTN search box:

In either case, you can use the default databse Nucleotide Collection (nr/nt) for the widest search and then click BLAST to run the search:


The following is the top of the resulting nucleotide BLASTN search:


Analyzing BLAST Results

Analysis of the rest of the BLASTN results are discussed in the BLAST Results page: View BLAST Results