Practical: BLAST of a nucleotide sequence.

This is a practical experiment steps to carry out BLAST search of a given nucleotide sequence.

(You can either watch the video or go through the steps mentioned below the video).

Follow These Steps:

Open NCBI home page http://www.ncbi.nlm.nih.gov/
Click on the text box which shows all databases and change it to "Nucleotide.
In the search box, type name of a protein or gene whose sequence you would like to retrieve. For example: Human Insulin.
Click on Home sapience at the right corner and you will get the list of all related Homo sapience.
Select whichever you want and click on it.
You will get the data in the format of Genbank. Since BLAST accepts only FASTA format, you need to change GenBank format to FASTA format by clicking FASTA. (just below the heading line).
The new page will appear where you will get the FASTA format of the nucleotide sequence.
Copy that sequence along with code present in the format. (Not the head line).
Go back to NCBI home page.
On the homepage, you will see an Option for BLAST. Click on it and BLAST homepage will open.
Click on the Nucleotide Blast.
When query window appears, paste the sequence you copied in the FASTA format.
After pasting, scroll down to the program selection and select Blastn.
Click on the BLAST.
Blast result will be displayed.
Result will show you the homologous sequences found and also you will get a graphical representation of the alignment with the query sequence.

NCBI Homepage

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