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Biological Information and Biological Databases

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Title: Biological Information and Biological Databases


1
Biological Information and Biological Databases
  • Meena K Sakharkar
  • Bioinformatics Centre
  • National University of Singapore

2
Biological Information
3
Nature of Life Science Information
  • Descriptive
  • Classification and Nomenclatural
  • Observational and Phenomenological
  • Experimental
  • Deduced/Computed
  • Simulated?
  • Theoretical?

4
Descriptive
5
Classify and Give Names
  • Classification and Nomenclature
  • Linnaeus - binomial nomenclature
  • Group into kingdoms, phyla, classes, orders,
    families, genera, species, subspecies, strains,
    etc
  • Associate descriptions to these classification
    schema, and classify according to description etc

6
Observational/Phenomenological
  • Like descriptive, yet more active
  • Observe a lot of biological phenomenon
  • Charles Darwin
  • Gregor Mendel to McClintock
  • Start to do some experiments

7
Experimental
  • From dissections to complex genetic engineering
    experiments

8
BioInformatics
  • Deduced/Computed
  • Simulated?
  • Theoretical?

9
What is BioInformatics?
  • Many related terms and buzzwords
  • A multiplicity of names
  • bioinformatics
  • biocomputing
  • biological computing
  • computational biology
  • computational genomics
  • biological data mining

10
Overview of the challenges of Molecular Biology
Computing
  • The huge dataset problem
  • automated DNA sequencers
  • the Human Genome Project
  • bulk sequencing of cDNAs (ESTs)

11
Human Genome Project
  • What is the Human Genome Project?
  • 15-year effort formally begun in October 1990.
    coordinated by the U.S. Department of Energy and
    the National Institutes of Health.
  • identify all the estimated 80,000 genes in human
    DNA,
  • determine the sequences of the 3 billion chemical
    bases that make up human DNA,
  • store this information in databases,
  • develop tools for data analysis, and
  • address the ethical, legal, and social issues
    (ELSI) that may arise from the project.

12
  • Who is head of the U.S. Human Genome Project?
  • The DOE Human Genome Program is directed by Ari
    Patrinos, and Francis Collins directs the NIH
    Human Genome Program.
  • Ari Patrinos also heads the Department of Energy
    Office of Biological and Environmental Research.

13
  • What are the comparative genome sizes of humans
    and other organisms being studied?

If compiled in books, the data would fill an
estimated 200 volumes the size of a Manhattan
telephone book (at 1000 pages each), and reading
it would require 26 years working around the
clock
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Informatics Data Collection and Interpretation
  • HUMAN GENETIC DIVERSITY
  • The Ultimate Human Genetic Database
  • Any two individuals differ in about 3 x 106 bases
    (0.1).
  • The population is now about 5 x 109.
  • A catalog of all sequence differences would
    require 15 x 1015 entries.
  • This catalog may be needed to find the rarest or
    most complex disease genes.

16
Databases
17
Basic Terminology
  • What is a nucleotide/protein sequence database
    and
  • databank?
  • Database is a collection of Nucleotide/protein
    sequence and their Associated annotations.
  • Databanks
  • Groups which collect, compile, maintain and
    distribute the database.

18
Fundamental Dogma
19
Work from the Code of Life
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Deduced and Computed Information in the Era of
Computational Biology
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Databases
  • What are the different kinds of databases and
    their formats?

Nucleic Acid Sequence EMBL at EBI.
GENBANK at NCBI. DDBJ at Japan.
Protein Sequence SWISS PROT NBRF(PIR)
24
Database
  • Protein structure databases
  • PDB
  • Information on the structural data for
    the proteins/nucleic acids.
  • whose 3-D structure solved by X-ray
    crystallography/NMR
  • PDB database
  • NRL 3D Database
  • NRL_3D is a sequence-structure database.
  • Can be used in conjunction with PIR.
  • PDB with PIR.

25
GenBank Entry
26
EMBL Entry
27
SwissProt Entry
28
Other databases
  • Genome Databases
  • GDB Genome Data Bank
  • OMIM
  • Pattern Databases
  • Prosite
  • TFD

29
Usage of databases
  • Annotation Searches - KW, Authors, Features.
  • What is the protein sequence for human insulin?
  • How does the 3D structure of calmodulin look
    like?
  • What is the genetic location of cystic fibrosis
    gene?
  • List all introns in rat?
  • Homology Searches
  • Is there any protein sequence that is similar to
    mine?
  • Is this gene known in any other species?
  • Has someone already cloned this sequence?

30
Usage of databases
  • Pattern searches
  • Does my sequence contain any known motif (that
    can give me a clue about the function)?
  • Which known sequences contain this motif?
  • Is any part of my sequence recoganised by a
    transcription factor?
  • List all known start, splice and stop signals in
    my genomic sequence
  • Prediction - Use the database as knowledge
    database
  • What may the structure of my protein be?
  • Secondary structure prediction
  • Modeling by homology
  • What is the gene structure of my genomic
    sequence?
  • Which parts of my protein have a high
    antigenicity?

31
Usage of Databases
  • Comparisons
  • Gene Families
  • Phylogenetic Trees

32
GenBank Growth Chart
Bases
Year
33
Evolutionary basis of Alignment
  • Enable the researcher to determine if two
    sequences display sufficient similarity to
    justify the inference of homology.
  • Similarity is an observable quantity that may be
    expressed as say identity or some other measure.
  • Homology is a conclusion drawn from this data
    that the two genes share a common evolutionary
    history.

34
Sequence Formats
35
Fasta Format
  • gtSANJAY REFORMAT of SANJAY.seq check 8826
    from 1 to 573 March 12, 1998
  • MASSSVPPMITEEEARFEAEVSAVESWWRTDRFRLTRRPYSARDVVSLRG
    TLHHSYASDQ
  • MAKKLWRTLKSHQSAGTASRTFGALDPVQVTMMAKHLDTIYVSGWQCSST
    HTATNEPGPD
  • LADYPYNTVPNKVEHLFFAQLYHDRKQHEARVSMTREQRAKTPYVDYLRP
    IIADGDTGFG
  • GATATVKLCKLFVERGAAGVHIEDQSSVTKKCGHMAGKVLVAVSEHINRL
    VAARLQFDVM
  • GVETVLVARTDAVAATLIQSNVDLRDHQFILGATNPDFKRRSLAAVLSAA
    MAAGKTGAVL
  • QAIEDDWLSRAGLMTFSDAVINGINRQLPEYEKQRRLNEWAAATEYSKCV
    SNEQGREIAE
  • RLGAGEIFWDWDIARTREGFYRFRGSVEAAVVRGRAFAPHADLIWMETSS
    PDLVECGKFA
  • QGMKASHPEIMLAYNLSPSFNWDAAGMTDEEMRDFIPRIAKMGFCWQFIT
    LGGFHADALV
  • TDTFAREFAKQGMLAYVERIQREERNNGVDTLAHQKWSGANYYDRYLKTV
    QGGISSTAAM
  • GKGVTEEQFKEESRTGTRGLDRGGITVNAKSRL

36
GCG Format
  • ckl.seq Length 473 September 15, 1999 1225
    Type P Check 8103 ..
  • 1 MSTKYSASAE SASSYRRTFG SGLGSSIFAG
    HGSSGSSGSS RLTSRVYEVT
  • 51 KSSASPHFSS HRASGSFGGG SVVRSYAGLG
    EKLDFNLADA INQDFLNTRT
  • 101 NEKAELQHLN DRFASYIEKV RFLEQQNSAL
    TVEIERLRGR EPTRIAELYE
  • 151 EEMRELRGQV EALTNQRSRV EIERDNLVDD
    LQKLKLRLQE EIHQKEEAEN
  • 201 NLSAFRADVD AATLARLDLE RRIEGLHEEI
    AFLRKIHEEE IRELQNQMQE
  • 251 SQVQIQMDMS KPDLTAALRD IRLQYEAIAA
    KNISEAEDWY KSKVSDLNQA
  • 301 VNKNNEALRE AKQETMQFRH QLQSYTCEID
    SLKGTNESLR RQMSEDGGAA
  • 351 GREAGGYQDT IARLEAEIAK MKDEMARHLR
    EYQDLLNVKM ALDVEIATYR
  • 401 KLLEGEESRI SLPVQSFSSL SFRESSPEQH
    HHQQQQPQRS SEVHSKKTVL
  • 451 IKTIETRDGE VVSESTQHQQ DVM

37
Taxonomy Database
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Blast Results
54
Examples of the New Biology
  • 1. Full genome-genome comparisons
  • 2. Rapid assessment of polymorphic genetic
    variations
  • 3. Complete construction of orthologous or
    paralogous groups of genes
  • 4. Structure determination of large
    macromolecular assemblies/complexes
  • 5. Dynamically simulation of realistic oligomeric
    systems
  • 6. Rapid structural/topological clustering of
    proteins
  • 7. Prediction of unknown molecular structures
    Protein folding
  • 8. Computer simulation of membrane structure and
    dynamic function
  • 9. Simulation of genetic networks and the
    sensitivity of these pathways to component
    stoichiometry and kinetics
  • 10. Integration of observations across scales of
    vastly different dimensions and organization to
    yield realistic environmental models for basic
    biology and societal needs

55
Theoretical?
  • The day will dawn when we will have sufficient
    information to understand how basic life
    functions are integrated into a living cell, and
    how such cells intercommunicate and interoperate
    to function as a living whole. Then maybe, we can
    start talking about theoretical biology

56
Categories of BioDbs - by domain of information
  • DNA
  • RNA
  • Protein
  • Genomic Mapping
  • Pathways
  • Structure
  • Bibliographic
  • Biochemical/Molecular/Miscellaneous

57
Other categories
  • By category of species
  • By families or superfamilies of molecules
  • etc
  • Demo
  • http//www.infobiogen.fr/services/dbcat/

58
Demonstration of BioDatabases
  • Majority of Life Science databases are online,
    accessible with Web via Internet
  • Catalogs of databases available
  • Need for a Registry to keep track and offer
    quality control
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