BS312 - Basic Local Alignment Search Tool – BLAST – Basic User ...

BS312 - Basic Local Alignment Search Tool – BLAST – Basic User Guidelines The use of „blast searching‟ via the NCBI website is probably the most commonly applied and regularly used bioinformatics analysis tool across laboratories the world over. Subsequently, very clear user guidelines are freely available via the blast help pages, in the form of the NCBI Handbook (Chapter 16: The BLAST Sequence Analysis Tool), which can be downloaded and kept as a *.PDF if required. Thus, the basic user guidelines below are designed simply to get you started and allow you to access and download the user manuals you require. In addition a brief, description of how to perform blast searches is provided.

1) Go to http://www.ncbi.nlm.nih.gov/

2) Click on “blast”

3) Click on “help”

4) Access the “NCBI Hanbook:Blast”

4) Download a *.PDF version of the Handbook for a clear user guide

5) To perform simple blast searches either re-follow steps 1 and 2, or go to http://blast.ncbi.nlm.nih.gov/Blast.cgi

There are four steps to a basic blast search: Basic search stratergy: (1) Choose the sequence (query) (2) Select the BLAST program (3) Choose the database to search (4) Choose optional parameters Then click “BLAST”

To choose your query sequence read the worksheet for details and access the file “BS312_blast_sequences.txt”.

6) To select a BLAST program click on the relevant link on the blast website

Different types of BLAST search • Nucleotide Blast – Blastn – search nucleotide database using a nucleotide query – MegaBlast – for nucleotide sequences that are very closely related (10 x faster than Blastn) • Protein Blast – Blastp – search protein database using an amino acid query • Blastx – search protein database using a translated nucleotide query • tBlastn – search translated nucleotide database using a protein query • tBlastx – search translated nucleotide database using a translated nucleotide query

7) Choose the database you wish to search

8) Choose optional parameters

You can limit your search by “organism”, by excluding “model” or “uncultured sequences” or by specifying a specific query to examine in the database. You can choose the exact form the blast algorithm takes. For example, you can use megablast or blastn. For this practical blastn will be preferred. You can also select your preferred parameters. See below.

9) Once you have setup your blast query click blast. Make sure that “Show results in a new window is selected” for ease of use in this practical.

10) Your query results will appear in a new window for you to examine.