You have been asked to construct a physical map of the baboon genome. What would be helpful in this task?

Question

A.  chromosome maps and STSs
B.  BLAST and ENCODE data    
C.  gene linkage data
D.  microarrays and SAGE

Clarify Question
· What is the key concept addressed by the question?
· What type of thinking is required?
· What key words does the question contain and what do they mean?

  Gather Content
· What do you already know about physical mapping?

  Consider Possibilities
· Consider the different answer options. Which can you rule out?

  Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?

  Reflect on Process
· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?

Answer 1

A.  chromosome maps and STSs

Clarify Question
· What is the key concept addressed by the question?
        o This question addresses physical mapping.
· What type of thinking is required?
        o This question is asking you to analyze the information given, using logic, to dissect the problem and determine the answer.
· What key words does the question contain and what do they mean?
        o A physical map is a map of the DNA itself, starting with clones and eventually down to the nucleotide level.

  Gather Content
· What do you already know about physical mapping?
        o The ultimate physical map is the base-pair sequence of an entire genome.
        o This is achieved by connecting clones into contigs, and eventually getting the detailed sequence of each.

  Consider Possibilities
· Consider the different answer options. Which can you rule out?
        o Would BLAST and ENCODE data be helpful for making a physical map? No, because these data help you interpret the structure and function of genes after the nucleotide sequence has been established.
        o Would gene linkage data be helpful for making a physical map? No, because gene linkage data provides a genetic map, but it needs to be aligned with the physical map to know real locations of genes.
        o Would microarrays and SAGE be helpful for making a physical map? No, because these tools allow you to analyze the transcriptome, but not the DNA structure of the genome.

  Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
        o Would chromosome maps and STSs be helpful for making a physical map? Yes. The chromosome maps represent a physical map of each chromosome. The STSs are sequence-tagged sites. STSs are short, unique stretches of DNA that are useful for aligning clones.

  Reflect on Process
· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?
        o This question asked what would help you to generate a physical map.
        o The question required you to analyze the information given, using logic, to dissect the problem and determine the answer.
        o Did you recognize that a physical map is a map of the DNA itself, and that chromosome maps and sequence-tagged sites would be most useful?