Iterated profile searching using PSI-BLAST

• Many proteins that are functionally and evolutionarily related but their sequences have diverged so much that this relationship is not easily identified by direct sequence comparison

• Thus, simple pair-wise sequence comparisons only detect a small proportion of distant evolutionary relationships.

• Many potentially interesting relationships are missed in simple FASTA, BLAST and Smith-Waterman searches.

• In these cases their sequence identity falls below the level required for inferring homology by ‘normal’ sequence comparison methods - called the twigh-light zone - about 25-30% sequence similarity.

• Comparison of three-dimensional protein structures would normally reveal such conserved relationships between two such proteins but 3D structures aren’t available for all proteins.

• More sensitive methods of searching for functional homologues of a protein are now starting to be developed.

• Position-Specific Iterated BLAST  (PSI-BLAST) is one such tool that takes advantage of a technique called profile searching as a more sensitive method of looking for protein function.

• PSI-BLAST is much better than normal BLAST when trying to detect sequences that are distantly related to your query sequence.

• More information on PSI-BLAST is available here:

Move on to: How does PSI-BLAST work?