HSL Bioinformatics Series - Beyond BLAST: Powering Up Your Sequence - Similarity Searches with NCBI PSI-BLAST AND PHI-BLAST
(Workshop 3 of 3)

Position-PSI Iterative (PSI) BLAST is a protein sequence search method that generates a protein search profile in place of the original BLAST algorithm. More importantly, you the searcher, choose the sequences you need to build the search profile for subsequent iterations. Pattern Hit Initiated (PHI)-BLAST BLAST is similar, with the notable exception that you can specify a protein motif or repeating protein element to build your protein profile. Both PSI-BLAST and PHI-BLAST provide a means to detecting distant functional relationships between proteins that are beyond the capability of BLAST. They are also the method of choice if “traditional” BLAST is returning too few of hits or unannotated hits. The recently re-formatted NCBI PHI- and PSI-BLAST interface and algorithms now put these powerful tools into the hands of all BLAST users. This two-hour workshop will work through the underlying concept of scoring matrices upon which PHI- and PSI BLAST are built upon and provide practical hands-on experience in PHI- and PSI-BLASTing.

Following this workshop you will be:

• Understand scoring matrices and their use in BLAST, PSI-BLAST and PHI-BLAST
• Know when and how to run PHI-BLAST and PSI-BLAST
• Able to link-out from PHI-BLAST results to discover gene and protein structural information for your query.