OR072: Assignment #3
1. Recall that a restriction enzyme cuts a DNA molecule at points in the base sequence exhibiting a
specific “word” of A/C/G/T bases. For example, a restriction enzyme might cut only after seeing the
sequence ATT.
a. How many possible sequences of length 3 are possible using the letters A,C,G, and T?
b. Assuming any one of these 3-letter “words” is equally likely to occur in a typical DNA
sequence, what are the chances of seeing the exact sequence ATT at a particular point in the
sequence?
c. Using the fact that the average number of steps you would take down a DNA strand before
hitting ATT is 1/(the chances of seeing ATT), on average how long would each fragment be
after cutting at all ATTs using this enzyme?
d. Try (a)-(c) for a four-base sequence, such as ATTG, to find out how big your fragments would
be. Continue this process to find out how big a “word” your restriction enzyme would need to
cut at, if you want to obtain DNA fragments of about size 1000. How about size 15,000?
2. Use the BLAST webpage to find the best match for the following DNA sequences. In each case, give
the first match that is a real organism (rather than a vector of some sort), give its E-value, and give the
common name for that organism.
mystery sequence #1
ATGTGCCATG TTAAGCGTAT TTAACACTGA TGATTACAGT CCAGCTGCGC AACAGAATAT
TCCTGCTCTC CGGAGAAGCT CTTCCTTCAT TTGCGCTGAA AGCTGTAGCT CTAAGTATCA
GTGTGAAGCA GGAGAAAACA GTAAAGGCAG CGTCCAGGAT AGAGTGAAGC GACCCATGAA
CGCATTCATT GTGTGGTCTC GGATCAGCAG GCGCAAGATG GCTCTAGAGA ATCCCAAAAT
GCGAAACTCA GAGATCAGCA AGCAGCTGGG ATACCAGTGG AAAATCCTTA CCGAAGCCGA
TAAATGGCCA TTCTTCCAGG AGGCACAGAA ACTACAGGCC ATGCATAGAG AGAAATACCC
GAATTATAAG TATCGACCTC GTCGGAAGGC GAAGATGCTG CAAAACAGTT GCAGTTTGCT
TCCGGCAGAT CCCTCTTCGG TCCCTGCCAG AGAAGTGTAC AACAACAGGT TGTACAGGGA
TGACTGTACC AAAGCCACGC ACTCAAGAAT GCAGCACCAG TTAGTCCACT TACCGCCCAT
CAACACAGCC AGCTCACCGC AGCAACGGGA CCGCTACAGC CACTCGATTC CAATCATATG
CCAAAGCTGT AG
Find the 6 errors in the best match, giving the location number of each error and whether it is a
mismatch, a gap in the databank sequence, or a gap in your sequence.
mystery sequence #2:
