(a) Distinguish between the programs BLASTP, BLASTN, BLASTX, TBLASTN,
TBLASTX of the BLAST package.
(b) Give a brief discussion of programs, PHI-BLAST, and PSI-BLAST. How is PSI- BLAST used in multiple sequence alignment?
A) blastp - protein blast, works with aminoacid chain database
blastn - nucleotide blast, works with nucleotide chain and compares it to nucleotide database
blastx - comparing translated nucleotides to protein database
tblastn - comparing protein chain to translated nucleotides database
tblastx - comparing and searching translated nucleotides to translated nucleotides database
B) PHI and PSI blast
(Position-Specific Iterative Basic Local Alignment Search Tool) derives a position-specific scoring matrix (PSSM) or profile from the multiple sequence alignment of sequences detected above a given score threshold using protein–protein BLAST.
PSI-BLAST provides a means of detecting distant relationships between proteins.
(Pattern-Hit Initiated BLAST) is a search program that combines matching of regular expressions with local alignments surrounding the match.
It may be preferable to just searching for pattern occurrences because it filters out those cases where the pattern occurrence is probably random and not indicative of homology