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CHOOSE optional parameters
output format
word size
expect value
E = Kmn e-λS
Extreme Value Distribution (EVD)
substitution matrix
Turn filtering on/off
Organism
different for every blast program
CHOOSE database
pnv_nr
Subtopic
Pat
Pdb
RefSeq
Swisprot
Month
nr
SELECT BLAST program
tblastx
tblastn
blastx
blastn
blastp
CHOOSE sequences
four component for BLAST search
X% identical
local alignment (distantly related protein)
global alignment (closely related protein)
X% divergence
one PAM (unit of evolution) = 1% amino acids changed between two proteins
at least 85% identical
probability of occurance + percent accepted mutations = mutation probability matrix
Trp
Cys
Leu
Phe
Tyr
Glu
Asp
Ser
Asn,