BLAST

BLAST is a primary sequence database that enables you to compare a DNA or protein sequence of interest to other known sequences, allowing you to find regions of similarity between them .  

The results of a BLAST search give a graphic summary of the amount of alignment between the query sequence and the sequence hits from the database. The database sequences which produce significant allignments are shown in a table, which tells you the protein that the sequence codes for. Each has an accession number; clicking on this accession number allows you to see the souce organism of the protien, as well as giving links to papers on the protein. The E value (Expect value) is the staistical significance threshold; it gives the number of hits that are likely to be found by chance, therefore a lower E value will result in better matches as the probability of a chance result is less.

The Blast web page can be found at: http://blast.ncbi.nlm.nih.gov/Blast.cgi

Basic Blast Programs

There are 5 different BLAST programmes depending on the type of sequence you are studying:  

A Table Showing a Brief Description of the Five Basic Blast Programmes

Nucleotide blast (blastn)	Search a nucleotide database using a nucleotide query
Protein blast (blastp)	Search protein database using a protein 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

 

BlastP, allows you to compare an amino acid query sequence against a protein database. BlastN enables you to look at a nucleotide query sequence against a nucleotide sequence database. Using BlastX you can compare a nucleotide query sequence translated in all reading frames against a protein sequence database. With tBlastN you can see the similarites between a protein query sequence and nucleotide sequences from the database, dynamically translated in all reading frames, and finally, tBlastX allows you to compare the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database .  Links to these programs can be found in the table above.

Specialised Blast Programs

There is also the option to perform more specialized BLAST searches such as a primer BLAST search. Links for these searches can be found below to main BLAST search links.