1. Basics of Comparative Genomics
Dr G. P. S. Raghava

2. AIM: To understand Biology of Organisms
Importance: More than 100 genomes sequenced, more than 250 in progress
Definition: Comparison of set of proteins of one genome to another genome + comparision of gene location, gene order and gene regulation
Application
Visualization of information on genome
Genome annotation (Prediction of gene, repeats, regulation region)
Evolutionary information (gene loss, duplication, horizontal gene transfer, ancestor)
Essential genes for cell survival
Classification of genes based on function
Tools and Databases

3. What is comparative genomics?
Analyzing & comparing genetic material from different species to study evolution, gene function, and inherited disease
Understand the uniqueness between different species

4. Why Comparative Genomics ?
It tells us what are common and what are unique between different species at the genome level.
Genome comparison may be the surest and most reliable way to identify genes and predict their functions and interactions.
– e.g., to distinguish orthologs from paralogs
The functions of human genes and other DNA regions can be revealed by studying their counterparts in lower organisms.

5. What is compared? Gene location Gene structure Gene characteristics
Exon number
Exon lengths
Intron lengths
Sequence similarity
Gene characteristics
Splice sites
Codon usage
Conserved synteny

6. Few facts from genome comparision
High degree of conservation of microbial proteins (~70% ancestral conserved region)
Protein related with ENERGY process are generally found all genomes
Proteins related to COMMUNICATION repersent repersent most distinctive function in each genome
INFORMATION related protein have complex behaviour
High frequence (~10%) non-orthologous gene displacement

7. Few Terminologies
Homology :- Homology is the relationship of any two characters ( such as two proteins that have similar sequences ) that have descended, usually through divergence, from a common ancestral character. Homologues are thus components or characters (such as genes/proteins with similar sequences) that can be attributed to a common ancestor of the two organisms during evolution.

8. Homologoues can either be orthologues xenologues, paralogues or.
Orthologues are homologues that have evolved from a common ancestral gene by speciation. They usually have similar functions.
Paralogues are homologues that are related or produced by duplication within a genome followed by subsequent divergence. They often have different functions.
Xenologues are homologous that are related by an interspecies (horizontal transfer) of the genetic material for one of the homologues. The functions of the xenologues are quite often similar.

9. Analogues
Analogues are non-homologues genes/proteins that have descended convergently from an unrelated ancestor. They have similar functions although they are unrelated in either sequence or structure.

10. Frequently used terms Homology
Orthologous: Common ancestral gene. They usually have similar functions
Paralogous: duplication of gene within genome have usually different functions
Xenologous: That are related by an interspecies (horizontal gene transfer) of the genetic material, have similar function
Analogous: Not evolve from same ancestor
Similarity: sequence similarity
Percent Identitity

11. Visualising Genome Information

12. Genome Annotation The Process of Adding Biology Information and
Predictions to a Sequenced Genome Framework

13. All-against-all Self-comparison
How?
Making a database of the proteome
Use each protein as a query in a similarity search against the database
(BLAST, WU-BLAST or FASTA)
Generate a matrix of alignment scores (P or E value)
: A conservative cutoff E value : 10e-6
Why?
Number of Gene Families
This comparison distinguishes unique proteins from proteins arisen from gene duplication, and also reveals the # of gene families.
Paralogs
Significantly matched pairs of protein sequences may be paralogs.

14. Between-Proteome Comparisons : Why?
To identify orthologs, gene families, and domains
Orthologs: (proteins that share a common ancestry & function)
A pair of proteins in two organisms that align along most of their lengths with a highly significant alignment score.
These proteins perform the core biological functions shared by the two organisms.
Two matched sequences (X in A, Y in B) may not be orthologs
(Y and Z are paralogs in B, X and Z are orthologs)
Identify true orthologs
highest-scoring match (best hit)
E value < 0.01
> 60% alignment over both proteins

15. Between-Proteome Comparisons: How?
Choose a yeast protein and perform a database similarity search of the worm proteome (WU-BLAST): a yeast-versus-worm search
Group the worm seqs that match the yeast query seq with a high P value (10-10 to ), also include the yeast query seq in the group
From the group made in 2, choose a worm seq and make a search of the yeast proteome, using the same P limit
Add any matching yeast seq to the group made in 2
Repeat 3 & 4 for all initially matched seqs in the group
Repeat 1-5 for every yeast protein
As 1-6, perform a comparable worm-versus-yeast search
Coalesce the groups of related seqs. and remove any redundancies so that every sequence is represented only once.
Eliminate any matched pairs in which less than 80% of each seq is in the alignment

16. Figure 1   Regions of the human and mouse homologous genes: Coding exons (white), noncoding exons (gray}, introns (dark gray), and intergenic regions (black). Corresponding strong (white) and weak (gray) alignment regions of GLASS are shown connected with arrows. Dark lines connecting the alignment regions denote very weak or no alignment. The predicted coding regions of ROSETTA in human, and the corresponding regins in mouse, are shown (white) between the genes and the alignment regions.

17. Target Validation
Target validation involves taking steps to prove that a DNA, RNA, or protein molecule is directly involved in a disease process and is therefore a suitable target for development of a new therapeutic compound.
Genes that do not belong to an established family are critical to many disease processes and also need to be validated as potential drug targets.