Practicum Review

1
Practicum Review

• Spring 07

2
Sequence Alignments

• Dot Plot
• Do it
• Be able to interpret results
• Classes of Algorithms what are they good for and
  why do we differentiate among them?
• Dynamic Programming
• Heuristic
• Examples
• Smith-Waterman
• Needleman-Wunsch
• BLAST

3
BLAST

• Variations of BLAST
• blastn,blastp, blastx, tblastn, tblastx
• Be prepared to use the right one on the NCBI
  website
• BLAST Algorithm
• How does BLAST work?
• How are substitution matrices used by BLAST?
• What advantages are there to protein comparisons
  using BLAST?
• Output
• How to interpret output
• What do the E-Value and Bit Score mean?

4
BLAST Example

• Given a DNA sequence, what variation of BLAST
  would you use to search a DNA database?
• Given a protein sequence, what variation of BLAST
  would you use to search a DNA database?
• Exercise in preparation for the exam
• Consider the protein your group studied on the
  Wiki
• Using your Human RefSeq Protein Accession Number,
  search for the Chimpanzee ortholog.
• What is the Human RefSeq Accession Number?
• What is the Chimpanzee RefSeq Accession Number?
• (If the Chimp ortholog doesnt yet seem to have
  been found, use another gene)
• Examine the alignment
• What is the sequence percentage similarity?
• What is the E-Value of the alignment?
• Do you consider that significant?
• Characterize t the differences in the sequences
  (if any)

5
EMBOSS

• What is it?
• How do you access it?
• Given a problem, can you find the appropriate
  program(s) to solve the problem?
• wossname
• Read The Manual for examples of
• Description
• Algorithm
• Input files
• Output files

6
EMBOSS Example

• Using the information from the prior BLAST
  example you found from your Wiki article
• If you are using protein sequences from RefSeq,
  get cDNA sequences from NCBI.
• Perform a dotplot of the human/chimpanzee
  sequences. What does the dotplot look like?
• Globally align the cDNA sequences.
• What program did you use for this?
• What differences can you point out from the
  alignment?
• Obtain the genomic DNA for the Human and
  Chimpanzee genes.
• Use ENTREZ Gene to get the genomic sequence
• Try to determine how many exons and their
  locations using one of the tools in EMBOSS (Hint
  Its a global alignment tool)
• Perform a dotplot of the cDNA and Genomic DNA.
  Does this result agree with what the alignment
  tool says?

7
Information Integration

• Go to the tutorial
• Be comfortable with the (right) answers

8
NCBI Workshop

• Go to the tutorial
• Be comfortable with the (right) answers

9
Phylogenetics

• Steps to perform an analysis
• Align sequences
• Calculate distance matrix
• Build tree from matrix
• Applications that perform the functions above

10
Structural Bioinformatics

• Be able to interpret output and the screens you
  may see. They will be similar to those you
  viewed in the tutorial
• Understand the data relationship between PDB and
  NCBI

11
Systems Biology

• Given information about a protein, be able to
  track that protein to fundamental pathways in
  KEGG
• Describe your strategy
• Describe the pathway or pathways you find
• Be able to interpret pieces of output

12
Micoarray

• Review Churchill article (in Sakai Resources)
• Consider an experimental design against
  Churchills advice

13
Sample Experiment

• Let us assume that we want to study the effects
  of a special diet (S) on mouse liver gene
  expression when compared to a regular diet (R).
  The study includes two strains of mice (A and B).
  Let us use the following convention
• AR represents a mouse of strain A on diet R
• AS for strain A on diet S
• BR for strain B on diet R and
• BS for strain B on diet S.
• Furthermore, when we write X ? Y, it means that
  the sample X is labeled with the green dye, the
  sample Y is labeled with the red dye, and these
  two samples are compared by (hybridized to) one
  microarray chip. The study uses the following
  design
• Four biologically independent replicates of AR ?
  AS, and
• Four biologically independent replicates of BR ?
  BS.
• What are the strength and weakness of this design?

14
Epigenetics of Stem Cell Development

• Review the Bernstein (2006) paper
• Be prepared to answer simple questions regarding
  techniques and interpretations.
• Samples
• The authors use antibodies specific to
  tri-methylated Lys4 or Lys27 of Histone H3. Why
  are these important reagents in this study?
• The authors observe changed patterns between stem
  cells and differentiated cells in what they call
  bivalent domains. What are these domains and
  what do the authors suggest that these
  differences mean?