Define PSI-BLAST and PHI-BLAST algorithms. How do they extend the functionality of the basic BLAST algorithm?

PSI-BLAST (Position-Specific Iterated BLAST) and PHI-BLAST (Pattern Hit Initiated BLAST) are two extensions of the basic BLAST (Basic Local Alignment Search Tool) algorithm, which is used in bioinformatics to compare primary biological sequence information.

1. PSI-BLAST: This algorithm allows the user to build a PSSM (Position-Specific Scoring Matrix) from the first set of BLAST alignments. This PSSM is then used to perform a new BLAST search. The process can be iterated several times, each time refining the PSSM. This iterative process allows PSI-BLAST to detect distant evolutionary relationships between sequences, which would be missed by the basic BLAST algorithm.

2. PHI-BLAST: This algorithm allows the user to input a pattern (a sequence of amino acids with some positions specified and others not) along with a sequence. The algorithm then finds all matches to the pattern in the sequence and uses these matches to initiate a BLAST search. This allows the user to find sequences that contain a specific pattern, which would not be possible with the basic BLAST algorithm.

In summary, both PSI-BLAST and PHI-BLAST extend the functionality of the basic BLAST algorithm by allowing the user to search for more specific or distant relationships between sequences.