Protein BLAST Introduction

To access the BLAST page in your live window, click on the NCBI icon in the upper left of the page (this takes you to the home page). Click on BLAST in the Popular Resources menu. Carefully read through the list of programs available under “Basic Blast” before proceeding.

BLAST Program Further details
nucleotide blast or blastn Compares a nucleotide query sequence against a nucleotide sequence database.
protein blast or blastp Compares an amino acid query sequence against a protein sequence database.
blastx Compares a nucleotide query sequence translated in all reading frames against a protein sequence database. You could use this option to find potential translation products of an unknown nucleotide sequence.
tblastn Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.
tblastx Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that the tblastx program cannot be used with the nr database on the BLAST Web page because it is computationally intensive.

Selecting a BLAST Program

The “Basic BLAST” menu allows you to do either nucleotide or protein BLAST searches of various types. Because our sequence is a protein sequence, we will do a Protein-protein BLAST (blastp). Click on this option in your live window, then click on NEXT on your tutorial page.