Bioinformatics Workshop

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Bioinformatics Workshop
by Lesly Guoan June 2004
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Instructures

• Chuck brown
• David Culley
• Steven Pechous
• Willem Rensink
• Tim Straub
• George Vandermark
• Ted Kisha

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Traveling

• Ching-Pa and Lin-Hai picked me and Olivia up in
  Neah Bay
• We forgot our medical release forms and had to
  get them
• We picked up Cynthia at Sappho and started the
  long drive to Richland
• The three of us tried to learn Chinese from
  Ching-Pa and Lin-Hai
• Ching-Pa and Lin-Hai brought us to a real Chinese
  restaurant to eat real Chinese food (the waiters
  laughed at our attempts to say hello and thank
  you in Chinese)
• We arrived at the hotel at 300am and woke up at
  700am to get ready for the first day of the
  workshop

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The Cartoon Guide to Genetics

• By Larry Gonick Mark Wheelis
• Also by Larry Gonick
• The Cartoon History of the Universe
• The Cartoon History of the United States
• The Cartoon Guide to Physics (with Art Hoffman)
• The Cartoon Guide to the Computer

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The Cartoon Guide to Genetics

• Touches on subjects that I learned in my biology
  class in a humorous, efficient way.
• Provides helpful visual aids when explaining a
  topic and transitions between new topics well
• Gets to the point quickly enough so I dont lose
  interest in the topic
• Covers a lot of material in a little space and
  doesnt lose information

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Men Who Advanced Genetics

• Fransesco Redi proved spontanious generation
  wrong
• Anton Leeuenhoek invented the microscope
  discovered sperm cells
• William Harvey ex ovo omnia meaning out of
  eggs, all
• Camerarius showed that flowers bore sex organs
• Gregor Mendel bred pea plants discovered
  alleles
• And many more

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Heredity

• Heredity, process of transmitting biological
  traits from parent to offspring through genes,
  the basic units of heredity. Heredity also refers
  to the inherited characteristics of an
  individual, including traits such as height, eye
  color, and blood type.
• Trait A particular aspect of the phenotype that
  can be measured or observed directly
• Heredity accounts for why offspring look like
  their parents when two dogs mate, for example,
  they have puppies, not kittens.
• Genetics is the study of how heredity works, in
  particular, of genes.
• A gene is a section of a DNA molecule, and it
  carries information for the construction of a
  protein or part of a protein.

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Interesting Dominant Recessinve Genes

• Brown eyes are dominant over blue ones
• Color vision is dominant over color blindness
• Hairy heads are dominant over bald ones
• The ability to curl the tongue over the inability
  to curl the tongue
• Extra fingers are dominant over 5 fingers
  (page 53 of The Cartoon Guide to Genetics)

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Gametes

• One of the differentiated cells that is a product
  of meiosis. In animals, sperm or egg cells.
• How it works (the 1st division)
• Cell starts with 46 chromosomes
• This is the diploid number, or 2 sets of
  chromosomes
• Chromosomes double to 92
• Cell divides so daughter cells have 46 again
• (the 2nd division) daughter cells divide,
  creating 2 new daughter cells each with 23
  chromosomes
• This is the haploid number, or 1 set of
  chromosomes
• Haploid cells only have 1 set of chromosomes,
  because they are gametes or sex cells

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Gametes Continued

• Gametes, or sex cells, only have 1 set of
  chromosomes, because they bind together to form a
  cell with 2 sets of chromosomes, one from the
  mother and one from the father

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National Center for Biotechnology Information

• Entrez
• Assess to sequence, mapping, 3D structure
  information
• Human Genome Resources
• Access to NCBIs annotated assembly related
  resources
• BLAST
• Access to BLAST family of sequence similarity
  search tools
• Comparative Genomics
• Access to complete genomes coomparison resources
• PubMed
• Access to biomedical literature

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BLAST Comparison

• Start at the TIGR website
• Using the gene indices button, select tomato from
  the plants tab
• Click on the identifiers or keywords button and
  copy paste the example code and click go
• Copy paste the gene sequence to the box
• In the database scroll box, click on potato, then
  click the submit BLAST job button
• The graph should look like this

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Agriculture

• Science is the foundation of agriculture
• Advances in scientific knowledge have driven, the
  impressive productivity of American agriculture
• United states is the worlds leading agricultural
  exporter
• All this possible as direct result of scientific
  advances through research

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Agriculture Continued

• USDA research has led to
• Better soil management
• Improved use of fertilizers
• Superior strains of seed
• Advanced control of insects, crop diseases, and
  weeds
• More efficient methods of harvesting, storing and
  transporting farm products to market
• (information from Science The Foundation of
  Agriculture, the USDA booklet we received on
  Monday)

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Alignment Matrix

• GACTGACTTATTG
• GAC---CTTATAG

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Thanks

• To Chuck Brown
• To David Culley
• To Ted Kisha (for the jokes)
• To the instructors
• To Ching-Pa and Lin-Hai
• To the USDA/ARS