Download Scoring matrices

Multiple sequence alignment
Jarno Tuimala
Scoring matrices
Uses of matrices
• Sequence alignment
• Database searches
• Phylogenetics
 Distances between sequences
 As evolutionary models
• For amino acids: PAM, Blosum, JTT…
• For DNA: IUB… (match 1.9, mismatch 0)
• For evolutionary work, matrices are replaced by
mathematical models, while working with DNA
sequence data
Muunnettu kuvista: http://www.bigchalk.com/cgi-bin/WebObjects/WOPortal.woa/wa/HWCDA/file?fileid=18373&flt=ga
Adeniini
Guaniini
Sytosiini
Tymiini
An example of a DNA matrix
•For local alignments with this matrix, gap opening -16 and
extension of -4 are typically used.
Sequence alignment
How to align sequences
• On paper / with computer
– Description of alignment for computer:
• scoring matrix
• gap penalties
• Aligning is not objective
– Check the results computer gives you!
• Alignments can be used for
– searching conserved sequence areas
– searching point mutations
– studying evolution of genes and species
Gap penalties
• Gap are evolutionarily expensive.
– Opening is more costly than extension
– Affine gap model
• Mathematically
– P = c + gd
– P is the total gap penalty
– c is gap opening penalty
– d is extension penalty
– g is the (lenght of the gap - 1)
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How to calculate an alignment
score?
match: +4
mismatch: -5
gap opening: -16
gap extension: -4
• 4+4+(-4)+4+(-16)+4+4+4+4+4 = 12
Multiple sequence alignment
(MSA)
What is MSA?
• MSA is an alignment generated from
three or more sequences.
• MSA is usually a global alignment, i.e.,
the aim is to align homologous residues
(nucleotides or amino acids) in columns
across the length of the whole
sequences.
A--GT
AC-GT
ACGGT
-CGGT
Alignability of sequences
• If the similarity of sequences drops too low,
sequences can’t be reliably aligned
(accuracy drops below acceptable).
– For proteins <20% similarity
– For DNA <~75% similarity
• This cut-off is called twilight zone.
• In other words, twilight zone marks the
sequence similarity below which the
observed similarity is mainly due to random
variation, and not due to evolution.
MSA and dynamic
programming
• There are methods that can produce
the optimal alignment (in terms of gap
penalties and scoring matrices), but
they are computationally very heavy.
– Program MSA uses dynamic programming
• In practise, dynamic programming
would be good for up to about 10
sequences, and is not usually used for
MSA.
– But for pairwise alignment it can be used.
MSA methods
• There are two popular methods to
perform a multiple sequence alignment:
– Progressive alignment
• Clustal (ClustalW and ClustalX), Pileup…
• Clustal is the most commonly used alignment
program
– Iterative alignment
• SAGA…
• We will review the Pileup method first
Progressive alignment
Progressive alignment
• Produce pairwise alignment between all the
sequences you want to align with MSA.
– Dynamic programming, ktup-methods, dot matrix
method…(you choose it)
• Produce a “guide tree” on the basis of the
pairwise distances calculated from pairwise
alignments.
– UPGMA, neighbor joining (you choose it)
• Produce an MSA using the guide tree.
– Sequences are aligned in the same order as the
guide tree instructs.
Pairwise alignments
Pairwise distances
No. of nucl. diffs.
Absolute distance,
used in Pileup/ Clustal
JC-distance
UPGMA
• Unweighted Pair Group Method with
Arithmetic mean
• One of the fastest and tree construction
methods
• Used in Pileup (GCG package)
• Clustal uses neighbor joining, but
calculating NJ tree is much more
demanding; thus, UPGMA is
demonstrated here
UPGMA tree
Constructing MSA
human
chimp
ACGTACGTCC
ACCTACGTCC
gorilla
ACCACCGTCC
orangutan ACCCCCCTCC
human
ACGTACGTCC
chimp
ACCTACGTCC
gorilla
ACCACCGTCC
orangutan ACCCCCCTCC
human
chimp
gorilla
orangutan
maqaque
ACGTACGTCC
ACCTACGTCC
ACCACCGTCC
ACCCCCCTCC
CCCCCCCCCC
Score of alignment
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•
1234
ACGT
ACGA
AGGA
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1: A-A + A-A + A-A = 1+1+1 = 3
2: C-C + C-G + C-G =1+0+0 = 1
3: G-G + G-G + G-G = 1+1+1 = 3
4: T-A + T-A + A-A = 0+0+1 =1
match=1
mismatch=0
• S(alignment) = S(1) + S(2) + S(3) + S(4) = 3+1+3+1 =
8
• The higher the score, the better the alignment
Progressive alignment - pros and
cons
• Pros
– Fast
– Quite accurate
• Cons
– Once gaps are opened they can never be
closed
• Errors in the alignment of the first few sequences
can have catastrophic effects on the whole
alignment
Muscle – both progressive
and iterative
Muscle algorithm
From http://nar.oxfordjournals.org/cgi/content/full/32/5/1792/GKH340F2
Muscle – comparison results
• As fast as Clustal, but at the same time:
• As accurate as T-COFFEE!
– T-COFFEE was previously the most accurate
alignment method (or software) available