how is psi blast implemented in phi blast and why?

PSI-BLAST (Position-Specific Iterated BLAST) is a variant of the BLAST algorithm that is used for searching protein databases. It works by creating a position-specific scoring matrix (PSSM) from the results of the first search, and then using this matrix for subsequent searches. This allows PSI-BLAST to find more distant relationships between proteins than standard BLAST.

PHI-BLAST (Pattern Hit Initiated BLAST) is another variant of the BLAST algorithm. It allows the user to specify a pattern that must be present in a sequence for it to be considered a match. This can be useful when searching for proteins that have a specific motif.

PSI-BLAST is implemented in PHI-BLAST in the following way:

1. The user specifies a pattern that must be present in a sequence for it to be considered a match. This is the same as in standard PHI-BLAST.

2. The first search is performed using this pattern. The results of this search are used to create a PSSM, just like in PSI-BLAST.

3. Subsequent searches are performed using the PSSM. This allows PHI-BLAST to find more distant relationships between proteins, just like PSI-BLAST.

The reason for implementing PSI-BLAST in PHI-BLAST is to combine the strengths of both algorithms. The pattern specification of PHI-BLAST allows for more targeted searches, while the PSSM of PSI-BLAST allows for the detection of more distant relationships. This makes PHI-BLAST a powerful tool for protein database searches.