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Dot Matrix

The document discusses the alignment of nucleotide and amino acid sequences, highlighting the importance of identifying matches, mismatches, and gaps in sequences for evolutionary analysis. It explains positional homology as a key concept in sequence alignment, which is essential for reconstructing evolutionary relationships. Various methods for alignment, including manual, dot matrix, and algorithmic approaches, are also outlined, along with their advantages and disadvantages.

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23 views

Dot Matrix

The document discusses the alignment of nucleotide and amino acid sequences, highlighting the importance of identifying matches, mismatches, and gaps in sequences for evolutionary analysis. It explains positional homology as a key concept in sequence alignment, which is essential for reconstructing evolutionary relationships. Various methods for alignment, including manual, dot matrix, and algorithmic approaches, are also outlined, along with their advantages and disadvantages.

Uploaded by

attasaiffaseeh456
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPT, PDF, TXT or read online on Scribd
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ALIGNMENT OF NUCLEOTIDE

&
AMINO-ACID SEQUENCES

1
An alignment is an evolutionarily meaningful
comparison of two or more sequences (DNA, RNA, or
proteins).

In the case of two DNA sequences, an alignment


consists of a series of paired bases, one base from
each sequence. There are three types of pairs:

(1) matches = the same nucleotide appears in both


sequences.
(2) mismatches = different nucleotides are found in
the two sequences.
(3) gaps = a base in one sequence and a null base in
the other.
GCGGCCCATCAGGTAGTTGGTG-G
GCGTTCCATC--CTGGTTGGTGTG
***..***** .*.******* *
2
Alignment: A hypothesis
concerning positional homology
among residues in a sequence.

Positional homology = A pair of nucleotides


from two aligned sequences that have
descended from one nucleotide in the
ancestor of the two sequences.

GCGGCCCATCAGGTAGTTGGTG-G
GCGTTCCATC--CTGGTTGGTGTG
***..***** .*.******* *
3
Positional homology = A pair of nucleotides
from two aligned sequences that have
descended from one nucleotide in the
ancestor of the two sequences.

GCGGCCCATCAGGTAGTTGGTG-G
GCGTTCCATC--CTGGTTGGTGTG
***..***** .*.******* *
4

These two nucleotides are derived from the


ancestor of cats and armadillos.
Homology:
The term was
coined by
Richard Owen
in 1843.

Definition:
Similarity
resulting from
common 5
Homology: A qualitative statment

• Homology designates a relationship of


common descent between entities
• Two genes are either homologs or not
• it doesn’t make sense to say “two genes are 43%
homologous.”
• it doesn’t make sense to say “Linda is 43% pregnant.”

6
Homology

By comparing homologous
characters, we can reconstruct
the evolutionary events that
have led to the formation of the
extant sequences from the common
ancestor. 7
Homology

When dealing with sequences, we are


interested in POSITIONAL
HOMOLOGY.

We identify positional homology by


ALIGNMENT. 8
ACTGGGCCCAAATC

A
ACTGGGCCCAAATC ACTGGGCCCAAATC
1 deletion
G A 1 insertion
1 substitution 1 substitution

ACTGGCCCAGATC ACAGGGCCACAAATC

Correct alignment Incorrect alignment

ACT-GGCC-CAGATC ACTGGCCCAGATC--
ACAGGGCCACAAATC ACAGGGCCACAAATC
**.-****-**.*** **.**.***.*..--
9
unknown

unknown unknown

ACTGGCCCAGATC ACAGGGCCACAAATC

Correct alignment? Incorrect alignment?


ACT-GGCC-CAGATC ACTGGCCCAGATC--
ACAGGGCCACAAATC ACAGGGCCACAAATC
**.-****-**.*** **.**.***.*..--
10
Sequence alignment = The
identification of the location of
deletion or insertions that might have
occurred in either of the two lineages
since their divergence from a common
ancestor.

Insertion + Deletion = Indel or Gap


11
Sequence alignment
1. Pairwise alignment
2. Multiple alignment

12
- Two DNA sequences: A and B.
- Lengths are m and n, respectively.
- The number of matched pairs is x.
- The number of mismatched pairs is y.

- Total number of bases in gaps is z.

13
An gap indicates that a deletion or an
insertion has occurred in one of the
two lineages.

GCGG-CCATCAGGTAGTTGGTG--
GCGTTCCATC--CTGGTTGGTGTG

14
The alignment is the first step in
many evolutionary and functional
studies.

Errors in alignment tend to amplify


in later computational stages.

15
Methods of alignment:
1. Manual
2. Dot matrix
3. Algorithmic (scoring matrices and gap
penalties)

16
Manual alignment.
nment When there
are few gaps and the two
sequences are not too different
from each other, a reasonable
alignment can be obtained by
visual inspection.

GCG-TCCATCAGGTAGTTGGTGTG
GCGTTCCATCAGGTGGTTGGTGTG
*** **********.********* 17
Advantages of manual alignment:
(1) use of a powerful and trainable tool
(the brain, well…, some brains).
(2) ability to integrate additional data,
e.g., domain structure, biological
function (e.g., 3D structure).

18
Disadvantages of manual alignment:

1. Subjectivity = the inability to formally


specify the algorithm.
2. Irreproducibility = the inability of two
researchers to reach the same result.
3. Unscalability = the inability to apply the
method to long sequences.
4. Incommensurability = the inability to
compare the results to those derived from
other methods.
19
The dot-matrix
method: The two
sequences are written
out as column and row
headings of a two-
dimensional matrix. A
dot is put in the dot-
matrix plot at a position
where the nucleotides
in the two sequences
are identical.

20
The alignment
is defined by a
path from the
upper-left
element to the
lower-right
element.

21
There are 4 possible steps in the path:
(1) a diagonal step
through a dot = match.
(2) a diagonal step
through an empty
element of the matrix =
mismatch.
(3) a horizontal step = a
gap in the sequence on
the top of the matrix.
(4) a vertical step = a gap
in the sequence on the
left of the matrix.

22
forbidden
directions

allowed
directions

23

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