Database Searching with BLAST

In this section you will perform a database search using one of the provided plant DNA sequences.

BLAST stands for Basic Local Alignment Search Tool. It is a computer method that takes a sequence provided by the user, called the query sequence, and searches a database of sequences to find close matches. The databases most often used are the public nucleotide sequence repositories located in North America (NCBI GenBank), Europe (EMBL), and Japan (DDBJ).

BLAST searches are conducted for a variety of reasons. You may want to find similar sequences in order to analyse their evolutionary history. Or, as in our case, you may want to find similar sequences whose structures and functions have been deciphered in order to make inferences about your query sequence.

You can run a Blast search against NCBI GenBank from within Geneious.

Click here to open one of the provided plant DNA sequences. Notice the sequence document provides nothing beyond the name and sequence and that there are no annotations on this sequence. By running a BLAST search with this sequence, we hope to find out what is known about this sequence or a close relative.

You can BLAST this sequence by clicking BLAST in the top tool bar. You should reset any changed parameters to their defaults by choosing Reset to Defaults under the settings button at the bottom left of the BLAST window - unless it is greyed out in which case you already have the defaults selected. We will run a BLAST search against the Nucleotide collection (nr/nt) database using the blastn program. The "nr" database refers to the "non-redundant" part of GenBank although this is historical only because the database is no longer non-redundant and contains all of the sequences found in GenBank+RefSeq Nucleotides+EMBL+DDBJ+PDB but no EST, STS, GSS or phase 0,1 or 2 HTGS sequences.

Keep all other settings in the BLAST options at their default values and click the search button. The search may take a few minutes to run.


Next page: Examine your search results

Exercise 2: Multiple Sequence Alignment
Exercise 3: Molecular Phylogenetics