Data-intensive Computing: Case Study Area 1: Bioinformatics

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Data-intensive Computing Case Study Area 1
Bioinformatics

• B. Ramamurthy

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Human Genetics

• Genomics
• Human Genome project
• Proteomics
• Diseasome
• Tree of life project
• Phylogenetics

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Human cell

• Base pair of DNA CG, AT
• C cytosine, G guanine, A adenine , T -
  thymine
• Each human cell contains approximately 3 billion
  base pairs.
• The DNA of a single cell contains so much
  information that if it were represented in
  printed words, simply listing the first letter of
  each base would require over 1.5 million pages of
  text!
• If laid end-to-end, the DNA strand measures about
  2 3 meters.
• DNA is a single large molecule at the nucleus of
  cell
• It is coiled a double helix
• Each strand of the DNA molecule is made of A, C,
  G and T example AAAGTTCTTAATTA that will be
  matched on the other strand by the matching base
  TTTCAAGAATTAAT
• These string of alphabets contain all the codes
  needed for the human functions
• Ref text Bioinformatics Databases, tools and
  algorithms, by. O. Bosu and S.K. Thukral

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More details

• Sequence of base pairs are grouped to make sense
  genes
• When a gene inside needs to be activated, the DNA
  molecule at the cell nucleus uncoils and unfurls
  to the right extent to expose that gene
• From the exposed ends of the DNA a RNA is formed.
• mRNA or messenger RNA is formed that carries with
  it the print of the open DNA section
• RNA and DNA differ in one respect RNA does not
  contain T or thymine but it has uracil (U). RNA
  is short-lived
• Once mRNA is formed open sections of the DNA
  close off.

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Protein formation

• mRNA travels to the cytoplasm where it meets the
  ribosome (rRNA)
• Ribosome reads the code in the mRNA (codon) and
  forms the amino acids.
• Twenty amino acids are prevalent in human cells.
  Ex codon GCU GCC GCA correspond to alanine
• In effect ribosome is a process control computer
  that takes in as input codons and produces amino
  acids as output.
• Amino acids polymerize and form polypeptide
  chains called proteins
• Proteins fold and form the basic structures such
  as skin and hair.
• Even though brain controls major human functions
  at the cell level it is the DNA that has the
  command and control.
• DNA is fixed code for a given human. (WORM
  characteristics)

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Lifes processes

• DNA is program that controls functions,
  operations and structure of a cell and in turn
  that of our life processes.
• Life processes are in fact dependent of the
  program in a DNA and the hundreds of millions of
  ribosomes.
• Life in this context appears as an immense
  distributed system.

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Bioinformatics

• Can we study, understand and analyze the
  complexity of the immensely complex system? Its
  structure and programs?
• University of Arizonas tree of life project
  (ToL) http//tolweb.org
• Human Genome project (NIH and DOE) collecting
  approximately 30,000 genes in human DNA and
  determining the sequences three billion bases
  that make up the human DNA.
• Out of the 30000 genes we do not know the
  functions of more than 50 of them.
• 99.9 of the nucleotide sequence is same for all
  of us
• 0.1 is attributed to individual differences such
  as race, color of skin, disposition to diseases
• High throughput sequencing is generating ultra
  scale biological data how to analyze this data?
• That is a data-intensive problem.

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Existing solutions?

• Traditional databases store, retrieve, analyze
  and/or predict huge biological data
• Software tools for implementing algorithms, and
  developing applications for in-silico experiments
• Visualization tools, user interfaces, web
  accessibility for search through data
• Machine learning and data mining methodologies.

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Databases

• Taxonomy DB
• Genomics
• Sequence db
• Structure db
• Proteomic database (PDB)
• Micro-array db
• Expression db
• Enzyme db
• Disease db
• Molecular biology db

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Tools

• Data analysis tools
• MySQL
• Perl
• Prediction tools
• Clustering
• Modeling tools
• Surface prediction, predicting area of interest,
  protein-protein interaction
• Alignment tools
• Many more http//galaxyproject.org/

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How can we help?

• How can we leverage our knowledge of large scale
  data management to address bioinformatics
  problems? DC methods.
• Large number of tools and data how we
  standardize the efforts so that they are
  complementary or repetitive? Cloud computing.

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Text Mining vs Genetic Sequence Mining (Dot plot)
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