Bioinformatics part 2

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Bioinformatics part 2

• Jon Manning
• Bioinformatics, QMRI

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Contents

• My background and skills
• Example projects
• Data transformation (Ann)
• Perl hackery Ensembl
• Structure/ mutation studies
• Data integration
• New and exciting Next Generation Sequencing

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Me!

• Background expertise
• Biochemistry
• Bioinformatics
• Sequence alignment analysis (PhD)
• Structural biology
• Perl hackery database mining
• Web interactivity
• Microarray (recent)

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Projects
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Data Transformation

• How do I convert this machine output to be
  readable by this software?

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Starting format
Annotation
Data
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Result
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Database Mining

• How can I download sequences for this big list
  of IDs?
• How can I look for this motif over the whole
  human genome? Can I allow for mis-match?

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Example Zinc finger nucleases (ZFNs)
TCCAGTAGCGAT N4-6 GAAGCTCAGTTC
http//www.sigmaaldrich.com/life-science/functiona
l-genomics-and-rnai/zinc-finger-nuclease-technolog
y/learning-center/what-is-zfn.html
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Programatic Tools

• Ensembl API
• Whole genome sequences
• Genes, transcripts, exons
• Variation (SNPs etc)
• Homology information
• Functional annotation
• Bioperl Automatic alignments, fetch sequences by
  ID etc
• Entrez utils Access NCBI resources

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Structure/ mutation / function

• What impact will making this change have on
  function?

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Simple ACE

• Reduced penetrance of malignant hypertension in
  Lewis vs Fischer rats.
• Localised to a QTL containing ACE
• Single amino acid change leucine (Lewis) to
  phenylalanine (Fischer)
• Could this change have caused a detrimental
  change in activity?

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No.
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Bit more complex PABP

• PABPC5 isnt transcriptionally active compared to
  PABPC1.
• Why doesnt a domain swap to replace eIF4G
  binding site work?
• Action
• Model PABPC5 RRM1-2 based on available structure
  for PABPC1
• Examine changes at known important residues
• Examine inter-domain interactions

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Data Integration

• How can I compare results over these disparate
  data sets??

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Example expression

• Different experimental techniques, with results
  keyed by different IDs
• Microarrays
• SAGE
• Sequencing
• Different values
• Counts from SAGE
• Intensities from microarrays
• Need to display and compare results

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Next Generation Sequencing
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What is next-gen sequencing?
J. Shendure and H. Ji. Next-generation dna
sequencing. Nat Biotechnol, 26 (10)11351145,
Oct 2008.
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Applications
J. Shendure and H. Ji. Next-generation dna
sequencing. Nat Biotechnol, 26 (10)11351145,
Oct 2008.
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Bioinformatics Challenges

• New statistics toolbox required
• Platform-specific error models (e.g.
  homo-polymers in 454)
• Tag frequency comparisons (diff. Exp.)
• Alignment assembly
• Short read lengths necessitate new methods
• Storage access

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Reporting
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Hypotheses

• Bioinformatics often hypothesis generation
• This set of genes may be important for this
  phenotypic difference
• These mutations probably have this effect on
  structure which might affect function this way
• Reduce experimental effort

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