Bioinformatics

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Bioinformatics

• 1. Origins
• 2. Definitions
• 3. Gene Expression Data
• 4. Comparative Genomics
• 5. Structural Functional Genomics

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Bioinformatics Origins

• 1. Large amounts of data from high throughput
  experiments, entire genome sequences, and
  measuring gene expression of entire genome
• 2. Lab note books impractical to store,
  analyze, display gene sequence expression
  data
• 3. Polymer nature of DNA, RNA, proteins favor
  mathematical analysis

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Bioinformatics Definitions

• 1. Broad- any use of computers to handle
  biological information
• 2. Computational Molecular Biology
• 3. Gene Expression Data
• 4. Comparative Genomics
• 5. Structural Functional Genomics

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Computational Molecular Biology

• 1. Use of computers to store, retrieve, analyze,
  or predict the composition and/or structure of
  biological compounds
• 2. Genomics- gene and genome sequences
• 3. Proteomics- proteins, gene expression
• 4. Metabolomics- products of protein mediated
  reactions, metabolic pathways

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Gene Expression Data

• 1. Compares expression of several genes in
  response to single environmental factor, example
  gradual O2 loss
• 2. Looks at each genes expression over time
  for genes with similar expression patterns
• 3. Fold change log transformation
• 4. Correlation Coefficient, r

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Fold Change Log Transformation

• 1. Ratio of experimental to control expression
  levels
• 2. Log2 or log10 of ratios compared in table

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Correlation coefficient, r

• 1. Values of 1 indicate perfect agreement
• 2. Values of -1 indicate expression of one gene
  represses another gene
• 3. Gene clusters

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Dendrogram

• 1. Diagram of genetic relatedness or evolutionary
  relationships
• 2. Horizontal distances indicate time
• 3. Vertical distances indicate DNA or
  evolutionary distances

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Gene Clusters

• 1. Identified by dendrograms

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Comparative Genomics

• 1. Differences and similarities between all genes
  of multiple species
• 2. Species clustered in dendrogram
• 3. Species relatedness or not
• 4. Evolutionary relationships

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Phylogenetic Dendrograms

• a. Two possibilities
  
• or
• b. Other possibilities

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Structural Functional Genomics

• 1. Structural- attempts to crystallize and/or
  predict the structures of all proteins in
  organism
• 2. Functional- identifies gene functions and
  associations of genes

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Ribosome (BioSci, 12-04)

• 1. Cellular organelle, translates genetic code
  into amino acids assembles them into proteins
• 2. Structure
• 3. 16s rRNA gene

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Ribosome Structure

• 1. Three separate strands of RNA with several
  dozen attached proteins
• 2. Large subunit
• 3. Small subunit

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Large Subunit

• 1. Two strands, one long one short
• 2. Long strand functions as ribozyme
• 3. Enzyme-like activity that helps form peptide
  bond between amino acids

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Small Subunit

• 1. Medium length RNA strand
• 2. Functional part of ribosome
• 3. Lines up tRNA anticodon with its complementary
  mRNA codon
• 4. Allows other end of tRNA its amino acid to
  interact with ribozyme of large subunit

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16s rRNA gene

• 1. Gene for small subunit RNA strand, strongly
  conserved
• 2. Woese, 1970, first used rRNA to demonstrate
  differences between bacteria archeae
• 3. Standard is all phylogenetic studies
• 4. Comparing 16s sequences can measure how long
  since two species have diverged

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16s Conservative Nature

• 1. rRNA genes not translated into proteins
• 2. Nucleic acid hybridization shows slow mutation
  rate
• 3. Strong selection maintains 16s crucial
  translation sequence
• 4. Parts of 16s sequence less crucial changes
  in them indicate divergence

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