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SCHOLARLY LITERATURE IN ARTS / HUMANITIES

von leslie mccall

Homology

Domain/motif

Pairwise sequence alignment

MUTATIONS

Mutability

low mutability

Tyr, Phe, Leu, Cys, Trp

high mutability

Asn, Ser, Asp, Glu

can happens by

deletion

insertion

substitution

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

four component for BLAST search

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

Swissprot

Month

nr

SELECT BLAST program

tblastx

tblastn

blastx

blastn

blastp

CHOOSE sequences

Blocks Substitution Matrix (Henikoff)

local alignment (distantly related protein)

X% identical

PAM

Percent Accepted Mutations (Dayhoff)

global alignment (closely related protein)

X% divergence

PAM1

probability of occurance + percent accepted mutations = mutation probability matrix

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

at least 85% identical

SCORES

scores

bit scores (normalized scores)

raw scores (calculate from substitution matrix)

gap penalty

extension - elongate gap

opening - inroduce gap

mismatch

identity

Functions