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Bio Lec 4

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Huma Tehreem
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7 views

Bio Lec 4

This is related to bioinformatics

Uploaded by

Huma Tehreem
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Introduction to

Bioinformatics
Profiles and Progressive AlignmentBy:Mirza A. Hammad
Profiles for families of sequences
can be built from MSAs
1 2 3
1 2 3
A 50% 75% 25%
C G — C 25% 0% 0%
A A T T 0% 0% 25%
A A A G 0% 25% 0%
— A — — 25% 0% 50%

Note: While profiles can be used for any kind of


sequence data, we’ll focus on protein sequences
Profiles

• Profile: A table that lists the frequencies of each amino acid in each
position of protein sequence

• Frequencies are calculated from a MSA containing a domain of interest

• Allows us to identify consensus sequence

• Derived scoring scheme allows us to align a new sequence to the


profile
• Profile can be used in database searches
• Find new sequences that match the profile

• Profiles also used to compute multiple alignments heuristically


• Progressive alignment
Profiles: Position-Specific Scoring
Matrix (PSSM)
• To compare a sequence to a profile, need to assign a
score for each amino acid

• The score the profile for amino acid a at position p is


M ( p , a )  f ( p , b )  s ( a , b )
20

where b 1

• f(p,b) = frequency of amino acid b in position p


• s(a,b) is the score of (a,b) (from, e.g., BLOSUM or PAM)
Profiles: PSSM

Insertion/deletion penalty
Gribskov et al. PNAS. 84 (13): 4355 (1987)
Profiles: Consensus Sequence

• A consensus residue C(p) is generated at each


position of the profile to aid the display of
alignments of target sequences with the profile

• The consensus residue c is the amino acid at p that


has the highest score M(p,c)

• c is the amino acid most mutationally similar to all the


aligned residues of the probe sequences at p, rather than
the most common one
Aligning a sequence to a profile
1 2 3 4 5
K L M – K
K .75 .25 .50
K L K L K
K M M L – L .75 .75
M L – L M M .25 .25 .50 .25
- .25 .25 .25
New sequence:
K K L L M
K K L - L M
K - L M – K
Align with profile: K - L K L K
K K L - L M K - M M L –
1 - 2 3 4 5 M - L – L M
Scoring a sequence-to-profile
alignment
• Score each column separately according to PSSM
• Each character contributes to score, weighed by its frequency

1 2 3 4 5 K K L - L M
K .75 .25 .50 1 - 2 3 4 5
L .75 .75
M .25 .25 .50 .25 Column 1 score:0.75 s(K,K) +
- .25 .25 .25
Profile-to-sequence alignments

• Optimum alignment can be found by dynamic programming


• Extension of Needleman-Wunsch

• Spaces are only added to msa – never removed


• Once a gap, always a gap

• Can align profiles to profiles


Evolutionary Profiles

• Profiles just seen are called average profiles

• Generally perform well, but disregard some of the


biology
• How did each position evolve?
• Amount of conservation varies from position to position
• Type of conservation varies from position to position

• Alternative: Evolutionary profiles


• Gribskov, M. and Veretnik, S., Methods in Enzymology
266, 198-212, 1996
Progressive multiple alignment
• Feng & Doolittle 1987, Higgins and Sharp 1988

• Idea: Sequences to be aligned are phylogenetically related


• these relationships are used to guide the alignment

• Popular implementations: CLUSTALW, PILEUP, T-Coffee


CLUSTALW

1. Perform pair-wise alignments between all pairs of sequences


(n x (n-1)/2 possibilities)

2. Generate distance matrix.


• Distance between a pair = number of mismatched positions in
alignment divided by total number of matched positions

3. Generate a Neighbor-Joining ‘guide tree’ from distance table

4. Use guide tree to progressively align sequences in pairs from


tips to root of tree.
• Actually, align profiles
• “Once a gap, always a gap”
CLUSTALW
CLUSTALW Tree

Tree calculated from an alignment of more than 1100 ring finger


domains, using ClustalW 1.83.
CLUSTALW heuristics
1. Individual weights are assigned to each sequence in a
partial alignment in order to downweight similar
sequences and up-weight highly divergent ones

2. Varying substitution matrices at different alignment stages


according to sequence divergence

3. Gaps
• Positions in early alignments where gaps have been opened
receive locally reduced gap penalties
• Residue-specific gap penalties and locally reduced gap penalties in
hydrophilic regions encourage new gaps in potential loop regions
rather than regular secondary structure.
Progressive Alignment:
Discussion
• Strengths:
• Speed
• Progression biologically sensible (aligns using a tree)

• Weaknesses:
• No objective function.
• No way of quantifying whether or not the alignment is good
Problems with CLUSTALW

• Local minimum problem:


• Alignment depends on sequence addition order

• With each alignment some proportion of residues are misaligned


• Worse for divergent sequences

• Errors get “locked in” and propagate as sequences are added

• Can result in arbitrary and incorrect alignments

• Clustal uses global alignment … may not be accurate for all parts of the
sequence
• T-Coffee considers local similarity as well as global
Iterative alignment

• To avoid local minima, realign subgroups of


sequences and then incorporate them into a
growing multiple sequence alignment

• Improves overall alignment score.


• May involve rebuilding the guide tree
• May be randomized

• Programs:
• MultAlin
• PRRP
• DIALIGN

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