Comparative genomics

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4 Οκτ 2013 (πριν από 4 χρόνια και 9 μέρες)

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Comparative genomics


Joachim Bargsten

February 2012



Comparative
genomics

The study of the relationship of genome structure and function

across different biological species or strains
.




Why
should we do this?


How
are we going to do this?

Study evolution






Resolve


Differences


Mechanism


Tree
of
life

http
://www.tolweb.org/tree/

Motivation


Transfer knowledge
from and to
simpler model organisms

Human

C.
elegans

Motivation

Overview


Molecular
phylogenetics


Multiple sequence alignment


Phylogenetic tree estimation


Ortholog prediction



Genome rearrangements


Large scale inversions, deletions and translocations


Synteny

&
Collinearity



Structural variations


Presented by Lin
Ke

Molecular
phylogenetics


The use of molecular data
to
establish
the relationship
between
species,
organisms or
gene
families


Homology

sequences
that share common
ancestry.

This is a all or nothing relation.

Sequences are never “a bit” homologous.



Orthologs
:

homologs in
different species
derived by
a speciation
event


Paralogs
: homologs
in the same or
different species derived by
a
duplication event

Homology

(co
-
)
orthologs

last

c
ommon

ancestor


Homology

inparalogs

last

c
ommon

ancestor


Homology

outparalogs

last

c
ommon

ancestor


Phylogenetic tree estimation


How do we estimate a phylogenetic tree?



Identify evolutionary conserved region



Multiple sequence alignment


MAFFT



Estimate the phylogenetic tree


PhyML

Phylogenetic tree estimation


Multiple sequence alignment

Phylogenetic tree estimation


Phylogenetic tree estimation


Infer evolutionary relationships

between species and genes/proteins



Rooted tree


Order of evolutionary

events




Unrooted

tree


Evolutionary relationships

between descendants

Non
-
coding regions


Phylogenetic
footprinting


Distantly related species


Phylogenetic shadowing


Closely related species



Use sequence comparison and

multiple alignment to find exons

and non
-
coding
functional

regions



E.g. Transcription factor

binding sites


What can we do with it?


Gene
annotation


Gene or protein function prediction


Identify non
-
coding elements in the genome


Species phylogeny


Genome evolution



Genome alignment


Pairwise alignment


Match chromosome sequence from species A to species B



Genome
alignment


dot plot


Dot
-
plot chromosome 2L tomato
-

potato

Synteny

&
collinearity


Synteny

gene loci are on the same chromosome



Conserved synteny

gene loci are on the same chromosome in different
species



Collinearity

The order of the gene loci is preserved across species

inverted

Resources


Comparative genomics plants


Plant
Genome Duplication
Database


http://chibba.agtec.uga.edu/duplication
/


Plaza


http
://bioinformatics.psb.ugent.be/plaza/

Exercise


ssh


X USERNAME@137.224.100.212



cd
/
mnt
/geninf15/work/bif_course_2012/
comparative_genomics_jwb


less assignment.txt

kwrite

assignment.txt