Pairwise sequence alignment

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Chapter 9: Subprograms

par Donaldo Cruz

Housestyle

par Brandon Robinson

Game Concept Map

par br br

Tech Neologisms

par Victoria Kapusenko

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