Nikolaj Blom

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Resources of Biomolecular Data Sequences,
Structures and Functionality PhD course 27803
Nikolaj Blom Center for Biological Sequence
Analysis BioCentrum-DTU Technical University of
Denmark nikob_at_cbs.dtu.dk
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Outline

• Magnitudes and Scales
• Resources Data Sources Tools
• Primary DNA sources
• Sequence Repositories
• Structure Repositories
• Functional Categorization
• Integration of Databases
• The Human Genome
• Genome Browsers
• Prediction Tools
• Evaluation of Prediction Servers
• Starting points
• Link collections

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Learning Objectives

• The student should be able to
• Describe differences between sequence
  repositories and curated databases
• Describe the challenges of maintaining
  genome-wide biological databases
• List two entry points for getting an overview of
  my gene of interest
• Describe how prediction servers may be evaluated

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Resources Sources Tools

• There is A LOT OF biomolecular databases/sources
• A LOT OF overlap of information/redundancy
• A LOT OF TOOLS
• Personal picks/preferences
• User-friendliness
• Update intervals
• Curation efforts / error correction
• Linkage to other DBs

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Faster than Moores law...
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Faster than Moores law...
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Human Genome Published HUGO Nature,
15.feb.2001 Celera Science, 16.feb.2001
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Magnitudes and Scales

• Human genome 3,200,000,000 bp
• Single basepair ? full genome is 9 orders of
  magnitude
• Genome Football field 3 billion leaves of
  grass
• Single base A T G C (or SNP) 1 leaf of grass
• Genome browsing
• Zooming from whole stadium to single leaf

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How we got the sequence

• Sanger chain termination method

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Primary DNA sources

• Trace files repositories
• Single read 500-1000 bp (golf ball size / jig
  saw puzzle)
• Variable quality
• WashU-Merck Human EST Project / Trace files
• Base-calling non-trivial

G, C or nothing?
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Assembly is Non-trivial!

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Sequence repositories - GenBank et al.

• GenBank / EMBL / DDBJ
• Highly redundant (many versions of same gene)
• Cross-updated daily
• Version history is recorded
• Previous sequence records can be retrieved
• Contigs/HTGS (100-200 kb) finishing at different
  stages
• Draft ? Finished
• Includes genomic DNA, cDNA, ESTs, translated
  peptides

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Non-redundant and Curated databases

• Non-redundant
• Manual or automatic curation
• DNA
• RefSeq (NCBI semi-automated)
• Ensembl gene index (automated)
• Protein
• RefSeq (NCBI semi-automated)
• TrEMBL (EMBL automated)

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Curated database UniProt/SwissProt

• SIB - Swiss Institute of Bioinformatics
• Protein Knowledgebase / Sequence Database
• Highly curated
• Experimental evidence evaluated (e.g.
  modifications)
• All 80,000 entries checked by Amos Bairoch
  himself -)
• ExPASy - Expert Protein Analysis System
• Proteomics tools links local servers

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Structure databases / Protein Data Bank (PDB)

• X-ray , NMR biomolecular structures
• Protein Data Bank (PDB)
• http//www.rcsb.org/pdb/

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Structure databases / Protein Data Bank (PDB)
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Functional Categorization

• Gene Ontology (GO)
• Hierarchical
• Controlled vocabulary

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Functional Categorization

• Gene Ontology (GO) http//www.geneontology.org/
• Molecular Function - the tasks performed by
  individual gene products examples are
  transcription factor and DNA helicase
• Biological Process - broad biological goals, such
  as mitosis or purine metabolism, that are
  accomplished by ordered assemblies of molecular
  functions
• Cellular Component - subcellular structures,
  locations, and macromolecular complexes examples
  include nucleus, telomere, and origin recognition
  complex

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Integration of databases - Webs of web-sites

• Links, links, links...
• SRS Sequence Retrieval System
• Powerful, complex query language
• BioDAS Distributed Annotation System

http//srs.ebi.ac.uk/
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For my gene, how do I

• Get an overview of the sequence information
  known? (GeneCardsOMIM)
• Examine the Genome Neighbourhood? (Genome
  Browsers)
• Predict protein post-translational modifications
  (PTMs)? (Prediction servers)
• (Evaluate the value of predicted features)

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GeneCards http//nciarray.nci.nih.gov/cards/
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GeneCards-II
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GeneCards-III
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GeneCards-IV
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GeneCards-V
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Genetic/Medical Information

• OMIM, Online Mendelian Inheritance in Man (NCBI)
• The OMIM database is a catalog of human genes and
  genetic disorders
• gt16,000 entries (April, 2006)
• Examples cystic fibrosis, prions, amyloid
  precursor protein
• Condensed, highly curated descriptions of
  genetics/disease/animal models/references

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OMIM-I (http//www3.ncbi.nlm.nih.gov/Omim/)
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OMIM-II
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OMIM-III
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For my gene, how do I

• Get an overview of the sequence information
  known? (GeneCardsOMIM)
• Examine the Genome Neighbourhood? (Genome
  Browsers)
• Predict protein post-translational modifications
  (PTMs)? (Prediction servers)
• (Evaluate the value of predicted features)

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Genome Browsing

• Three public
• Open access
• Use same genome build/assembly
• NCBI (U.S.)
• UCSC (Santa Cruz, U.S.)
• EnsEmbl (EBI, EU)
• (One private)
• (Restricted, commercial closed 2005)

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Celera Discovery System Database
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Genome Browsers - Portals to the Genomic World

• UCSC Univ. California Santa Cruz (U.S.)
• http//genome.ucsc.edu/
• NCBI National Center for Biotechnology
  Information (U.S.)
• http//www.ncbi.nlm.nih.gov/Genomes/index.html
• EnsEmbl European Molecular Biology Laboratory
  (E.U.)
• http//www.ensembl.org/

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UCSC Genome Browser
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UCSC Genome Browser II
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NCBI
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NCBI
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EnsEmbl Genome Browser
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EnsEmbl Genome Browser
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EnsEmbl Genome Browser
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EnsEmbl Genome Browser
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EnsEmbl Genome Browser
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EnsEmbl Genome Browser
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For my gene, how do I

• Get an overview of the sequence information
  known? (GeneCards)
• Examine the Genome Neighbourhood? (Genome
  Browsers)
• Predict protein post-translational modifications
  (PTMs) or Gene Structure? (Prediction servers)
• ...and evaluate the reliability of prediction
  methods

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CBS Services/Toolbox http//www.cbs.dtu.dk/service
s/
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NetPhos a prediction server
http//www.cbs.dtu.dk/services/NetPhos/
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NetPhos a prediction server
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Evaluating Prediction Servers

• Performance on independent/cross-validated data
  presented?
• Published in peer-reviewed journal?
• Cited by others?
• Science Citation Index
• Linked to from credible web sites?
• Google Page-rank
• linkURL search

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Evaluating Prediction Servers
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2can Bioinformatics Education

• At EBI European Bioinformatics Institute
• http//www.ebi.ac.uk/2can/index.html
• Tutorials, resource links, etc.

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EnsEMBL Bioinformatics Education
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Starting Points

• General Bioinformatics
• NCBI, National Center for Biotechnology
  Information, U.S.
• EBI, European Bioinformatics Institute
• Prediction Tools
• CBS, DK
• Expasy (Protein analysis), Switzerland

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Dynamic Resources

• Pros
• Includes most recent developments
• Updated regularly
• User interface improves(usually)
• Cons
• Difficult to keep pace
• Tutorials and lectures hard to recycle -(
• Difficult to use at irregular intervals

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Genome Browsers - Portals to the Genomic World

• Three main entry points
• NCBI, UCSC, EnsEmbl
• Essentially contain same information
• High degree of linking to secondary databases
• Advisable to become familiar with only one genome
  browser
• Learn to navigate and make queries
• GeneCards and OMIM
• well suited for getting a quick overview of a
  gene of interest

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Prediction Servers

• Evaluate scientific soundness
• Look for indications of quality (citations, etc.)
• Remember that prediction servers provide...well,
  predictions!

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Learning Objectives

• The student should be able to
• Describe differences between sequence
  repositories and curated databases
• Describe the challenges of maintaining
  genome-wide biological databases
• List two entry points for getting an overview of
  my gene of interest
• Describe how prediction servers may be evaluated

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Immediate Feedback
Title Resources of Biomolecular Data
Sequences, Structures and Functionality

• Did the lecture live up to your expectations?
• Did you expect to learn about resources that were
  not covered during this lecture?
• NB! You can also provide input at the general
  course evaluation

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The End
25,000?