pairwise sequence alignment

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Pairwise Sequence Alignment

sequence alignment

gaps #

gap penalties

extension

opening

deduction for gaps

G + Ln

for insertion & deletion

to improve alignment between two sequence

identity and similarity

quantitative inference

homology

orthologs

common ancestor

paralogs

gene duplication

alignment algorithms

local sequence

BLAST

component

4. choose optional parameter

3. choose database

nucleotide sequence database

protein sequence database

2. select BLAST programme

types

tblastx

translated nucleotide --> translated nucleotide

tblastn

protein --> translated nucleotide

blastx

translated nucleotide --> protein

blastp

protein --> protein

blastn

nucleotide --> nucleotide

1. choose query

accession number

FASTA format

best for sequence that share some similiraty or different length

region of greater similarity

global sequence

best for highly similar of sequence similar length

entire length of sequence

scoring matrices

TYPES

BLOSUM

BLOSUM 30

longer weaker local alignment

BLOSUM 80

detect known member of protein family

BLOSUM 62

most effective in finding potential similarities

BLOSUM 90

short alignment, highly similar

perform better than PAM

most sensitive detect structural of functional substitution

directly calculated, no extrapolation

PAM

Dayhoff Model

to compare divergent proteins compute

based on global alignment of closely related proteins