problem set for regular expressions

[Sofia Robb]

Hello All,

One of the students thought it would be helpful if i supplied a "quiz" or something similar so that you would work on it and then give it back to me when finished so that I can see your progress and make suggestions.

so here is it. 

Problem Set

1. The enzyme ApoI has a restriction site: R^AATTY where R and Y are degenerate nucleotideides. See the IUPAC table to identify the nucleotide possibilities for the R and Y.

   Write a regular expression that will match occurrences of the site in a sequence. (hint: what are you going to do about the actual cut site, represented by the '^'?)



2. Use the regular expression you just wrote to find all the restriction sites in the following sequence. Be sure to think about how to handle the newlines!

   GAATTCAAGTTCTTGTGCGCACACAAATCCAATAAAAACTATTGTGCACACAGACGCGAC
   TTCGCGGTCTCGCTTGTTCTTGTTGTATTCGTATTTTCATTTCTCGTTCTGTTTCTACTT
   AACAATGTGGTGATAATATAAAAAATAAAGCAATTCAAAAGTGTATGACTTAATTAATGA
   GCGATTTTTTTTTTGAAATCAAATTTTTGGAACATTTTTTTTAAATTCAAATTTTGGCGA
   AAATTCAATATCGGTTCTACTATCCATAATATAATTCATCAGGAATACATCTTCAAAGGC
   AAACGGTGACAACAAAATTCAGGCAATTCAGGCAAATACCGAATGACCAGCTTGGTTATC
   AATTCTAGAATTTGTTTTTTGGTTTTTATTTATCATTGTAAATAAGACAAACATTTGTTC
   CTAGTAAAGAATGTAACACCAGAAGTCACGTAAAATGGTGTCCCCATTGTTTAAACGGTT
   GTTGGGACCAATGGAGTTCGTGGTAACAGTACATCTTTCCCCTTGAATTTGCCATTCAAA
   ATTTGCGGTGGAATACCTAACAAATCCAGTGAATTTAAGAATTGCGATGGGTAATTGACA
   TGAATTCCAAGGTCAAATGCTAAGAGATAGTTTAATTTATGTTTGAGACAATCAATTCCC
   CAATTTTTCTAAGACTTCAATCAATCTCTTAGAATCCGCCTCTGGAGGTGCACTCAGCCG
   CACGTCGGGCTCACCAAATATGTTGGGGTTGTCGGTGAACTCGAATAGAAATTATTGTCG
   CCTCCATCTTCATGGCCGTGAAATCGGCTCGCTGACGGGCTTCTCGCGCTGGATTTTTTC
   ACTATTTTTGAATACATCATTAACGCAATATATATATATATATATTTAT

   
   


3. Determine the site(s) of the cut in the above sequence. Print out the sequence with "^" at the cut site.

   Hints:

   • Use subpatterns (parentheses and $1, $2) to find the cut site within the pattern.
   • Use s///
   
   Example: if the pattern is GACGT^CT the following sequence

   would be cut like this:
   AAAAAAAAGACGT^CTTTTTTTAAAAAAAAGACGT^CTTTTTTT
   



4. Now that you've done your restriction digest, determine the lengths of your fragments and sort them by length (in the same order they would separate on an electrophoresis gel).

   Hint: take a look at the split man page or think about storing your matches in an array. With one of these two approaches you should be able to convert this string:
   

      AAAAAAAAGACGT^CTTTTTTTAAAAAAAAGACGT^CTTTTTTT

   
   into this array:
   

   ("AAAAAAAAGACGT","CTTTTTTTAAAAAAAAGACGT","CTTTTTTT")