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

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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

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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.

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What is compared?

• Gene location
• Gene structure
• Exon number
• Exon lengths
• Intron lengths
• Sequence similarity
• Gene characteristics
• Splice sites
• Codon usage
• Conserved synteny

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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

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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.

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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.

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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.

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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

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Visualising Genome Information
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Genome Annotation

• The Process of Adding Biology Information and
• Predictions to a Sequenced Genome Framework

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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.

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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 lt 0.01
• gt 60 alignment over both proteins

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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 10-100), 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

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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.
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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.

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