Pairwise sequence alignment

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Pairwise sequence alignment

SCORES

scores

bit scores (normalized scores)

raw scores (calculate from substitution matrix)

gap penalty

extension - elongate gap

opening - inroduce gap

mismatch

identity

SCORING MATRICES

BLAT

more than 95% similarity

design to rapidly align longer nucleotide sequence

500 times faster than BLAST

BLAST-like alignment tool

BLAST

Smith-Waterman local alignment

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

Blocks Substitution Matrix (Henikoff)

X% identical

local alignment (distantly related protein)

PAM

Percent Accepted Mutations (Dayhoff)

global alignment (closely related protein)

X% divergence

PAM1

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

MUTATIONS

Mutability

Trp

Cys

Leu

Phe

Tyr

high mutability

Glu

Asp

Ser

Asn,

Can happens by

deletion

insertion

substitution