3. Pairwise alignment Flashcards
1
Q
alignment score
A
is used to measure the quality of the alignment
2
Q
dot plot
A
intrasequence comparison
3
Q
more than 40% identity
A
homology!
4
Q
20-40% identity
A
homology probable
5
Q
below 20% identity
A
homology possible but unlikely
6
Q
sliding window approach
A
- remove noise
- compare multiple residues at the same time
- only a dot if nmatcg within wsize
7
Q
best scoring alignment
A
optimal alignment
8
Q
next best scoring alignment
A
suboptimal alignment
9
Q
the optimal alignment is not necessarily
A
correct
10
Q
scoring systems (3)
A
- theoretical, count nr of mutations
- physiochemical properties
- based on evidence from evolution
11
Q
Substitution matrices
A
Eg PAM and Blosum
12
Q
PAM stands for
A
point accepted mutation
13
Q
PAM
A
- based on observed aa substitution frequencies
- logP(aa1->aa2)
- several matrices, number represent how many accepted mutations
- 1 PAM - 1 accepted aa change/100 residues
14
Q
Blosum
A
- derived from multiple local alignments
- should reflecr evolutionary events if alignment is correct
- eg BLOSUM 62 is a matrix calculated from comparisons of sequences with no more than 62% identical
15
Q
PAM-
Blosum-
A
evolutionary distance
sequence similarity
