Types of Similarity sequences, 1. Homology ( Homologous sequences ) Orthology ( Orthologous sequences ) Paralogy ( Paralogous sequences ) 2. Analogy ( Analogous sequences ) 3. Xenelogy ( Xenelogous sequences ) All explained briefly with examples.

1. ALIGNMENT OF PAIRS OF SEQUENCEALIGNMENT OF PAIRS OF SEQUENCE
( Types of Similarity Sequences )( Types of Similarity Sequences )
By,By,
Rahul M. PrathapRahul M. Prathap
11stst
year M.Sc Bioinformaticsyear M.Sc Bioinformatics

2. What’s in this presentation ?

What is Sequence alignment ?

Types of Similarity Sequences

Homology

Orthology

Paralogy

Analogy

Xenelogy

3. Let’s find out....

4. What is Sequence alignment ?

It is a way of arranging the sequences of DNA, RNA, or
protein to identify regions of similarity.

It may be a consequence of functional, structural, or
evolutionary relationships between the sequences.
Eg:-
GOPGOPI VARUNVARUN_ _ - ( Red : Mismatch )- ( Red : Mismatch )
GOPGOPY VARUNANVARUNAN - ( Green : Gaps )- ( Green : Gaps )

5. 
Aligned sequences of nucleotide or amino acid residues
are typically represented as rows within a matrix.

An alignment between two sequences is simply a pairwise
match between the characters of each sequence.

A true alignment of nucleotide or amino acid sequences is
one of that reflects the evolutionary relationship between
two or more homologs (sequences that share a common
ancestor).

If characters are similar due to convergent evolution we
call it as Analogs.

6. Homology

Homologous genes are genes that derive from a common
ancestor.

Homologous genes can arise through a variety of different
biological processes.
Speciation Gene duplication

7. 
Pairs of homologous genes derived by speciation which
results in two homologous genes diverging in different
lineages are described as Orthologous and called
Orthologs.

Homologous genes which arise by gene duplication, the
process by which a gene becomes copied, within the same
genome are described as paralogous, and are called
paralogs, which can be more formally defined as a pair of
genes whose most recent common ancestor occurred
immediately before a gene duplication event.

8. Orthology

Sequences which are inferred to be descended from the
same ancestral sequence separated by a speciation event:
when a species diverges into two separate species.

Speciation — is the phenomenon during which a common
ancestor gives birth to two subgroups that slowly drift away
from their common genetic makeup to become distinct
species.

9. 
The term "ortholog" was coined in 1970 by the molecular
evolutionist Walter Fitch.

10. 
These genes in different species originated by vertical
descent from a single gene of the last common ancestor.

Biologists usually expect orthologs to have similar
functions and structure.

11. In the figure below, A1 and A2
are orthologs, and so are B1 and B2.

12. Let’s see some examples....

13. Arabidopsis thaliana (Thale Cress) Chlamydomonas (Green algae)
The plant Flu regulatory protein is present both in Arabidopsis (multicellular
higher plant) and Chlamydomonas (single cell green algae). The Chlamydomonas
version is more complex: it crosses the membrane twice rather than once, contains
additional domains and undergoes alternative splicing. However it can fully
substitute the much simpler Arabidopsis protein, if transferred from algae to plant
genome by means of genetic engineering. Significant sequence similarity and
shared functional domains indicate that these two genes are orthologous
genes, inherited from the shared ancestor.

14. Paralogy

Paralogs are homologues separated by a duplication
event, meaning that within a genome, a gene was
duplicated.

One of the duplicates may have kept the original function
while the other duplicate could have acquired a new
function.

Mechanism of gene duplication allows these sequences to
evolve different functions.

15. A1 and B1 are paralogs in the figure shown below.

16. The hemoglobin gene of
humans and the
myoglobin gene of
chimpanzees are
Paralogs.
The four known
classes of
hemoglobins
(hemoglobin A,
hemoglobin A2,
hemoglobin B, and
hemoglobin F) are
paralogs of each other.
While each of these
proteins serves the
same basic function of
oxygen transport, they
have already diverged
slightly in
function: fetal
hemoglobin
(hemoglobin F) has a
higher affinity for
oxygen than adult
hemoglobin.

17. Analogy

If similarity between sequences arises due to convergent
evolution, those genes are called Analogs.

Convergent evolution creates analogous sequences that
have similar form or function but were not present in the
last common ancestor of those groups.

18. In 2013 the first genome-wide study of convergence was published. Comparisons of
the genomes of echolocating bats and the dolphin identified numerous convergent
amino acid substitutions in genes implicated in hearing and vision.

19. Xenelogy

Homologs resulting from horizontal gene transfer between
two organisms are termed xenologs.

Xeno is a Greek word that means “foreigner”. It is also
coined by Walter Fitch.

Xenologs result from a lateral transfer between two
organisms — a direct DNA transfer between two species.

Xenologs can have different functions, if the new
environment is vastly different for the horizontally moving
gene.

20. A typical case of lateral transfer (or xenologs) is the acquisition of the isoleucyl-
tRNA synthase from their host by several bacteria. The isoleucyl-tRNA synthase
is a protein involved in the synthesis of other proteins, and its acquisition by
bacteria seems to help them becoming antibiotic resistant. When this happens,
the newly acquired isoleucyl-tRNA synthase is a xenolog of the other tRNA
synthases contained in the bacteria.

21. Thank You !!!!Thank You !!!!