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Return to Nov 29-Dec 5

Chapter Exercises 8,9,10

Exercises from Chapter 8
(Schematics only, for now)


1.Choose file to download from a database.
2.Open the file.
3.Read the data.
4.Perform the required steps to extract seq. data from  whichever form  the 
  data is in.
   1.Initialize variables (counter, hash)
   2.Using the counter, march through the list of genes.
     a.Populate the hash: For each gene, make the gene name the key and its 
       sequence (or gene ID) the value.
6.While input value is not null, ask user for gene-name input.
  a.Search the hash for the gene name using the subroutine.
  b.Return the value.
  c.Print value and ask user for the next gene name.


1.Receive codon argument and eplode into array.
2.For each position
  a.Use mutation subroutine to make 3 mutations at that position.
  b.Add new codon to an array which holds values of the mutated codons.
3.For each array element
  a.Use dna2aa subroutine to return the amino acid that would result.
  b.Print: when 'original codon'  is mutated to 'new codon', 'aa' results. 

Exercises from Chapter 9


1.Before the file read-in in Ex9-3, add a read from command line function.
2.If command line is null, prompt user to input a file name.
  a.Return to file read-in function.
4.(The read-in value is REBASE, whether from command line or from file)
5.Once the data has been read in prep it to be read (discard headers/blanks/etc)
6.Use split to separate the name and  recognition site fields.
7.Populate a hash using the name as key and rec. site as value.


(for single or multiple sites)
1.Load the entire sequence.
2.Search the sequence for restriction enzyme sites.
3.At each restriction site found, change sequence text to a different color,
  with each color assigned to a particular enzyme.
4.Print out the new colored sequence and the color legend.

(for overlapping sites)

Is it possible to print layers of text above the sequence? Probably but I 
don't know how!

Exercises from Chapter 10