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 CHAPTER 12 PROBLEMS
   
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QUESTIONS ON SCRIPT EXAMPLE 2óBIOPERL: USING THE GLOB FUNCTION TO OBTAIN A LIST OF FILES NAMED WITH A SPECIFIED EXTENSION (p. 580)
  1. What EMBOSS program would you use to rearrange a DNA sequence while retaining its initial composition? What would be a reason for doing so?
  2. What are some other EMBOSS programs that would be interesting to run on a mutated sequence?
  3. Modify the check_cpg subroutine so that it also outputs the identity and length in base pairs of the sequences. Test this by downloading a few sequences into one file instead of individual files and running the script on a file containing multiple sequences.
  4. Modify the script so that it cleans up after itself by removing the ".cpg" and ".mut" files it creates.
  5. Modify the check_cpg subroutine so that it returns the length of the longest CpG island, and add code to the main script that computes the overall maximum CpG island length for all of the sequences and prints this information.
  6. Write a BioPerl script that uses SeqIO to read a FASTA file of sequences and Bio::Factory::EMBOSS to find the longest orf in each sequence.




 

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