Homology

SCORES

identity

mismatch

gap penalty

opening - inroduce gap

extension - elongate gap

scores

raw scores (calculate from substitution matrix)

bit scores (normalized scores)

SCORING MATRICES

PAM

PAM1

probability of occurance
+
percent accepted mutations
=
mutation probability matrix

at least 85% identical

one PAM (unit of evolution) =
1% amino acids changed between two proteins

Percent Accepted Mutations (Dayhoff)

global alignment (closely related protein)

X% divergence

BLAST

Blocks Substitution Matrix (Henikoff)

local alignment (distantly related protein)

X% identical

Smith-Waterman local alignment

four component for BLAST search

CHOOSE sequences

SELECT BLAST program

blastp

blastn

blastx

tblastn

tblastx

CHOOSE database

nr

Month

Swissprot

RefSeq

Pdb

pat

Subtopic

pnv_nr

CHOOSE optional parameters

different for every blast program

organism

turn filtering on/off

substitution matrix

expect value

Extreme Value Distribution (EVD)

E = Kmn e-λS

word size

output format

BLAT

BLAST-like alignment tool

500 times faster than BLAST

design to rapidly align longer nucleotide sequence

more than 95% similarity

MUTATIONS

can happens by

substitution

insertion

deletion

Mutability

high mutability

Asn, Ser, Asp, Glu

low mutability

Tyr, Phe, Leu, Cys, Trp