BLAST can be used to search sequence databases to find those sequences that are most similar to any given query sequence. BLAST stands for Basic Local Alignment Search Tool. This is particularly useful if you have an unknown DNA sequence and want to find out what it may code for. It is also useful in taxonomy if you want to find the most closely related species. BLAST searches can be carried out with either nucleotide sequences (blastn) or protein (blastp) sequences.
Select the unknown sequence file, then click the 
BLAST button.
Select the Nucleotide Collection (nr/nt) database and choose the blastn program, then click the search button on the right. This will BLAST to the whole Genbank database (excluding EST, STS, GSS, WGS, and TSA). More specific NCBI databases are available under the database chooser.
Like all databases if many people are accessing it simultaneously then output can be slow. Be patient. An estimate of the approximate search time will appear just below the toolbar. Once the search is complete the results will appear in the Document Table. Sort the results by the "E Value" column, from lowest to highest E Value, by clicking on the column header (if it is already sorted by this column you will see a triangle next to the column name). Then click on the first (or top) Genbank "hit" to display the result in the Alignment View below.
The viewer shows the query aligned to the hit. Note that in this case there is an exact match, AF483338. Click on the Query Centric View tab above the document table to see all the hits aligned to the query.
Now click back to the Hit table, select the top match and click on Download Full Sequences. This will download the complete Genbank sequence for the hit. The full sequence is displayed in the Sequence View tab, with the region that corresponds to the BLAST hit annotated on it. You can still also display the BLAST alignment by clicking on the Alignment View tab.
For a more detailed tutorial on BLAST, please see our BLAST Searching tutorial