Revision as of 14:41, 24 March 2006

TUTORIAL - BLAST

In this Tutorial you will learn to:

• Set up and perform a Blast search.

• Decipher the Output.

• Analyze the results.

OVERVIEW

A reason why you may want to do a BLAST Query may be that you have found an interesting marker, so you want to retrieve it's gene, and see what it is related to.

BLAST searches are divided into categories according to the nature, and size of the input query and the primary goal of the search.

A BLAST search has four components:

• Query

• Data Base Program

• Search Purpose

• Goal

For the purpose of this tutorial use the file "NM _024426-Wilms.Fasta" provided in the tutorial data directory. This is a nucleotide sequence file. There is a second file which contains the corresponding protein sequence "NP_077744-Wilms.fasta".

Provide a little background info about Wilm's tumor. (It was chosen at random).

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• In the Visualization Area click on the Sequence Alignment tab.

• Click on the Blast button.

Note that the result displays the length of the longest sequence selected (here there is only one)due to the sample.

Click on the drop down arrow and select a program. Since this is a nucelotide query, we want to select a nucleotide query program such as blastn.

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There are five different types of queries you can run, depending on what data you are using: