sequence comparison with dot matrices

8/2/2019 Sequence Comparison With Dot Matrices

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Computational Biology, Part 2Sequence Comparison with Dot

Matrices

Robert F. Murphy

Copyright 1996, 1999-2006.All rights reserved.


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Sequence Alignment

Definition: Procedure for comparing two or

more sequences by searching for a series of

individual characters or character patternsthat are in the same orderin the sequences

Pair-wise alignment: compare two sequences

Multiple sequence alignment: compare morethan two sequences


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Example sequence alignment

Task: align abcdef with abdgf

Write second sequence below the first

abcdefabdgf

Move sequences to give maximum match betweenthem

Show characters that match using vertical bar


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abcdef

||abdgf

Insert gap between b and d on lower

sequence to allow d and f to align


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abcdef

|| | |ab-dgf


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abcdef

|| | |ab-dgf

Note e and gdont match


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Matching Similarity vs. Identity

Alignments can be based on finding only

identical characters, or (more commonly)

can be based on findingsimilarcharacters

More on how to definesimilarity later


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Global vs. Local Alignment

We distinguish

Global alignment algorithms which optimize

overallalignment between two sequences

Local alignment algorithms which seek only

relatively conservedpieces of sequence

Alignment stops at the ends of regions of strong

similarity

Favors finding conserved patterns in otherwise

different pairs of sequences


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Global vs. Local Alignment

Global

LGPSSKQTGKGS-SRIWDN

| | ||| | |LN-ITKSAGKGAIMRLGDA

Local

--------GKG--------

|||--------GKG--------


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Why do sequence alignments?

To find whether two (or more) genes or

proteins are evolutionarily related to each

other

To find structurally or functionally similar

regions within proteins


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Origin of similar genes

Similar genes arise bygene duplication

Copy of a gene insertednext to the original

Two copies mutateindependently

Each can take on separatefunctions

All or part can betransferred from one part

of genome to another


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Methods for Pairwise Alignment

Dot matrix analysis

Dynamic Programming

Word ork-tuple methods (FASTA and

BLAST)


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Sequence comparison with dot

matrices Goal: Graphically display regions of

similarity between two sequences (e.g.,

domains in common between two proteinsof suspected similar function)


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Sequence comparison with dot

matrices Basic Method: For two sequences of

lengths M and N, lay out an M by N grid

(matrix) with one sequence across the topand one sequence down the left side. For

each position in the grid, compare the

sequence elements at the top (column) andto the left (row). If and only if they are the

same, place a dot at that position.


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Examples for protein sequences

(Demonstration A6, Sequence 1 vs. 2)



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Interpretation of dot matrices

Regions of similarity appear as diagonal

runs of dots

Reverse diagonals (perpendicular todiagonal) indicate inversions

Reverse diagonals crossing diagonals (Xs)

indicate palindromes(Demonstration A6, Sequence 4 vs. 4)


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Interpretation of dot matrices

Can link or "join" separate diagonals to

form alignment with "gaps"

Each a.a. or base can only be used onceCan't trace vertically or horizontally

Can't double back

A gap is introduced by each vertical orhorizontal skip


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Uses for dot matrices

Can use dot matrices to align two proteins

or two nucleic acid sequences

Can use to find amino acid repeats within aprotein by comparing a protein sequence to

itself

Repeats appear as a set of diagonal runs stackedvertically and/or horizontally



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Uses for dot matrices

Can use to find self base-pairing of an RNA

(e.g., tRNA) by comparing a sequence to

itself complemented and reversed Excellent approach for finding sequence

transpositions


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Filtering to remove noise

A problem with dot matrices for long

sequences is that they can be very noisy due

to lots of insignificant matches (i.e., one A) Solution use a window and a threshold

compare character by character within a

window (have to choose window size)require certain fraction of matches within

window in order to display it with a dot


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Example spreadsheet with

window (Demonstration A7)


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How do we choose a window

size? Window size changes with goal of analysis

size of average exon

size of average protein structural element

size of gene promoter

size of enzyme active site


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How do we choose a threshold

value? Threshold based on statistics

using shuffled actual sequence

find average (m) and s.d. () of match scores ofshuffled sequence

convert original (unshuffled) scores (x) toZscores

Z = (x - m)/

use threshold Z of of 3 to 6

using analysis of other sets of sequences

provides objective standard of significance


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Dot matrix analysis with DNA

Strider (Mount, Fig 3.4) Get phage l cI and phage P22 c2 repressor

sequences from Genbank (X00166 and

V01153 respectively) Use DNA Strider 1.4 (contact TA to get a

copy)

Use window size of 11 and stringency of 7


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Dot matrix (Mount Fig 3.4)

Note set ofdiagonals

in lowerright thatdo not lineup due to

insertionnear 475on cI

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Dot matrix analysis with DNA

Strider (Mount, Fig 3.6) Get human LDL receptor protein sequence

from Genbank (P01130)

Use weighting Identity




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W=1 S=1

Note set of

stackeddiagonalsin upperleft

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W=23 S=7

Note set of

stackeddiagonalsin upperleft

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Reading for next class

Mount, Chapter 3 through page 93

Look over paper by Needleman and

Wunsch on web site

(03-510/710) Durbin et al, pp 17-32

sequence comparison with dot matrices

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