1-Month Practical Master Course

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1-Month Practical Master Course Genome
AnalysisJaap Heringa Centre for Integrative
Bioinformatics VU (IBIVU) Vrije Universiteit
Amsterdam The Netherlands www.ibivu.cs.vu.nl heri
nga_at_cs.vu.nl
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Biological Sequence AnalysisPair-wise sequence
alignment Residue exchange matrices Multiple
sequence alignment Phylogeny
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DNA sequence
.....acctc ctgtgcaaga acatgaaaca nctgtggttc
tcccagatgg gtcctgtccc aggtgcacct gcaggagtcg
ggcccaggac tggggaagcc tccagagctc aaaaccccac
ttggtgacac aactcacaca tgcccacggt gcccagagcc
caaatcttgt gacacacctc ccccgtgccc acggtgccca
gagcccaaat cttgtgacac acctccccca tgcccacggt
gcccagagcc caaatcttgt gacacacctc ccccgtgccc
ccggtgccca gcacctgaac tcttgggagg accgtcagtc
ttcctcttcc ccccaaaacc caaggatacc cttatgattt
cccggacccc tgaggtcacg tgcgtggtgg tggacgtgag
ccacgaagac ccnnnngtcc agttcaagtg gtacgtggac
ggcgtggagg tgcataatgc caagacaaag ctgcgggagg
agcagtacaa cagcacgttc cgtgtggtca gcgtcctcac
cgtcctgcac caggactggc tgaacggcaa ggagtacaag
tgcaaggtct ccaacaaagc aaccaagtca gcctgacctg
cctggtcaaa ggcttctacc ccagcgacat cgccgtggag
tgggagagca atgggcagcc ggagaacaac tacaacacca
cgcctcccat gctggactcc gacggctcct tcttcctcta
cagcaagctc accgtggaca agagcaggtg gcagcagggg
aacatcttct catgctccgt gatgcatgag gctctgcaca
accgctacac gcagaagagc ctctc.....
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Genome size

• Organism Number of base pairs
• ?X-174 virus 5,386
• Epstein Bar Virus 172,282
• Mycoplasma genitalium 580,000
• Hemophilus Influenza 1.8 ? 106
• Yeast (S. Cerevisiae) 12.1 ? 106
• Human 3.2 ? 109
• Wheat 16 ? 109
• Lilium longiflorum 90 ? 109
• Salamander 100 ? 109
• Amoeba dubia 670 ? 109

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Three main principles

• DNA makes RNA makes Protein
• Structure more conserved than sequence
• Sequence Structure Function

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Regulation, signalling cascades, chaperonins,
compartmentalisation
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How to go from DNA to protein sequence
A piece of double stranded DNA 5
attcgttggcaaatcgcccctatccggc 3 3
taagcaaccgtttagcggggataggccg 5
DNA direction is from 5 to 3
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How to go from DNA to protein sequence
6-frame translation using the codon table (last
lecture) 5 attcgttggcaaatcgcccctatccggc
3 3 taagcaaccgtttagcggggataggccg 5
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Evolution and three-dimensional protein structure
information
Isocitrate dehydrogenase The distance from the
active site (in yellow) determines the rate of
evolution (red fast evolution, blue slow
evolution)
Dean, A. M. and G. B. Golding Pacific Symposium
on Bioinformatics 2000
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Protein Sequence-Structure-Function
Ab initio prediction and folding
Sequence Structure Function
Threading
Function prediction from structure
Homology searching (BLAST)
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Widely used tool for homology detection PSI-BLAST

• Heuristic tool to cut down computations required
  for database searching (1M sequences in DB)
• Sensitivity gained by iteratively finding hits
  (local alignments) and repeating search

Q
hits
DB
T
PSSM
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Threading
Template sequence
Compatibility score
Query sequence
Template structure
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Threading
Template sequence
Compatibility score
Query sequence
Template structure
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Fold recognition by threading
Fold 1 Fold 2 Fold 3 Fold N
Query sequence
Compatibility scores
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Bioinformatics

• Nothing in Biology makes sense except in the
  light of evolution (Theodosius Dobzhansky
  (1900-1975))
• Nothing in bioinformatics makes sense except in
  the light of Biology

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Divergent evolution

• Ancestral sequence ABCD
• ACCD (B C)
  ABD (C ø)
• ACCD or ACCD
  Pairwise Alignment
• AB-D A-BD

mutation deletion
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Divergent evolution

• Ancestral sequence ABCD
• ACCD (B C)
  ABD (C ø)
• ACCD or ACCD
  Pairwise Alignment
• AB-D A-BD

mutation deletion
true alignment
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Mutations under divergent evolution
G
(a)
G
(b)
Ancestral sequence
G
C
A
C
One substitution - one visible
Two substitutions - one visible
Sequence 1
Sequence 2
G
(c)
G
(d)
1 ACCTGTAATC 2 ACGTGCGATC D 3/10
(fraction different sites (nucleotides))
G
A
A
A
Back mutation - not visible
Two substitutions - none visible
G
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Convergent evolution

• Often with shorter motifs (e.g. active sites)
• Motif (function) has evolved more than once
  independently, e.g. starting with two very
  different sequences adopting different folds
• Sequences and associated structures remain
  different, but (functional) motif can become
  identical
• Classical example serine proteinase and
  chymotrypsin

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Serine proteinase (subtilisin) and chymotrypsin

• Different evolutionary origins, no sequence
  similarity
• Similarities in the reaction mechanisms.
  Chymotrypsin, subtilisin and carboxypeptidase C
  have a catalytic triad of serine, aspartate and
  histidine in common serine acts as a
  nucleophile, aspartate as an electrophile, and
  histidine as a base.
• The geometric orientations of the catalytic
  residues are similar between families, despite
  different protein folds.
• The linear arrangements of the catalytic residues
  reflect different family relationships. For
  example the catalytic triad in the chymotrypsin
  clan (SA) is ordered HDS, but is ordered DHS in
  the subtilisin clan (SB) and SDH in the
  carboxypeptidase clan (SC).

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A protein sequence alignment MSTGAVLIY--TSILIKECHA
MPAGNE----- ---GGILLFHRTHELIKESHAMANDEGGSNNS
A DNA sequence
alignment attcgttggcaaatcgcccctatccggccttaa att---
tggcggatcg-cctctacgggcc----

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What can sequence tell us about structure (HSSP)
Sander Schneider, 1991
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Searching for similarities What is the function
of the new gene? The lazy investigation (i.e.,
no biologial experiments, just bioinformatics
techniques) Find a set of similar protein
sequences to the unknown sequence Identify
similarities and differences For long proteins
identify domains first
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• Evolutionary and functional relationships
• Reconstruct evolutionary relation
• Based on sequence
• -Identity (simplest method)
• -Similarity
• Homology (common ancestry the ultimate goal)
• Other (e.g., 3D structure)
• Functional relation
• Sequence Structure Function

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Searching for similarities
Common ancestry is more interesting Makes it
more likely that genes share the same
function Homology sharing a common ancestor a
binary property (yes/no) its a nice tool When
(an unknown) gene X is homologous to (a known)
gene G it means that we gain a lot of information
on X what we know about G can be transferred to
X as a good suggestion.
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Biological definitions for related sequences

• Homologues are similar sequences in two different
  organisms that have been derived from a common
  ancestor sequence. Homologues can be described
  as either orthologues or paralogues.
• Orthologues are similar sequences in two
  different organisms that have arisen due to a
  speciation event. Orthologs typically retain
  identical or similar functionality throughout
  evolution.
• Paralogues are similar sequences within a single
  organism that have arisen due to a gene
  duplication event.
• Xenologues are similar sequences that do not
  share the same evolutionary origin, but rather
  have arisen out of horizontal transfer events
  through symbiosis, viruses, etc.

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How to evolve

• Important distinction
• Orthologues homologous proteins in different
  species (all deriving from same ancestor)
• Paralogues homologous proteins in same species
  (internal gene duplication)
• In practice to recognise orthology,
  bi-directional best hit is used in conjunction
  with database search program (this is called an
  operational definition)

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So this means
Source http//www.ncbi.nlm.nih.gov/Education/BLAS
Tinfo/Orthology.html
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Example today Pairwise sequence alignment needs
sense of evolution Global dynamic programming
MDAGSTVILCFVG
Evolution
M D A A S T I L C G S
Amino Acid Exchange Matrix
Search matrix
MDAGSTVILCFVG-
Gap penalties (open,extension)
MDAAST-ILC--GS
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How to determine similarity Frequent evolutionary
events at the DNA level 1. Substitution 2.
Insertion, deletion 3. Duplication 4. Inversion
We will restrict ourselves to these events
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nucleotide one-letter code
A DNA sequence alignment attcgttggcaaatcgcccctatcc
ggccttaa att---tggcggatcg-cctctacgggcc----
A protein sequence
alignment MSTGAVLIY--TSILIKECHAMPAGNE----- ---GGIL
LFHRTHELIKESHAMANDEGGSNNS

amino acid one-letter code
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Dynamic programmingScoring alignments
Substitution (or match/mismatch) DNA
proteins Gap penalty Linear gp(k)ak
Affine gp(k)bak Concave, e.g.
gp(k)log(k) The score for an alignment is the
sum of the scores over all alignment columns
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Dynamic programmingScoring alignments
Sa,b - gp(k) gapinit
k?gapextension affine gap penalties
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DNA define a score for match/mismatch of
letters Simple Used in genome
alignments
A C G T
A 1 -1 -1 -1
C -1 1 -1 -1
G -1 -1 1 -1
T -1 -1 -1 1
A C G T
A 91 -114 -31 -123
C -114 100 -125 -31
G -31 -125 100 -114
T -123 -31 -114 91
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Dynamic programmingScoring alignments
T D W V T A L K T D W L - - I K
20?20
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Affine gap penalties (open, extension)
Amino Acid Exchange Matrix
Score s(T,T)s(D,D)s(W,W)s(V,L)-Po-2Px
s(L,I)s(K,K)