5. Multiple sequence alignment Flashcards
1
Q
Consensus sequences
A
uses more information than pairwise alignment
2
Q
PROSITE patterns
A
generating the consensus profile
- > database for motifs and patterns
- > rules for describing patterns
3
Q
SYNTAX
R
A
Required residue
4
Q
SYNTAX
x
A
any residue
5
Q
[ ]
A
multiple residues allowed
6
Q
{ }
A
residues not allowed
7
Q
x(i,j)
A
residues repeated i-j times
8
Q
frequency table
A
tabulate how common a nucleotide/residue is in every position
9
Q
PSSM abbr
A
position specific scoring matrices
10
Q
ppsm
A
- known residue preference at each alignment position
- pssm values are weighted sums of standard substitution matrices
- to further extend previous search, to find more family members
11
Q
Logos
A
- Tall column height - high conservation
- Short column height - low conservation
- letter height is for each residue
12
Q
Iterated sequence searches
A
- discover known sequences in family
- not possible to detect all with one sequence
13
Q
PSI-BLAST
A
Position-specific iterated BLAST
- BLAST, use E-value cutoff to select sequences
- Iterate until convergence
a. make PSSm
b. search database
14
Q
Hidden Markov Models
A
- weather etc
- probability of eg sequence etc.
15
Q
one of most common MSA
A
progressive alignment
