Given the following DNA sequence: GGTGTAAAGAATCTT a. Construct a keyword tree b. Construct a suffix tree 2.

.  Given the following DNA sequence: GGTGTAAAGAATCTT

a.      Construct a keyword tree

b.     Construct a suffix tree

2. How many different nucleotide sequences may code for the following protein sequence:

           Arg-Lys-Pro-Val-Ser-Ile-Ala?

3.  Given the following MSA (Multiple Sequence Alignment), describe (in pseudocode) how you would determine which positions contained informative sites :

AT-ACGCCGATGCAT

ATTACGACGATGCTT

ATTACGACGAAGCTT

AT-ACGACGATGCAT

4. Describe how gene finding algorithms work. Include a description of all the elements that they search for to help determine whether or not a sequence is a protein coding gene

5. What is BLAST? Describe how the algorithm works. Be sure to include any statistical measures that are used in determining the strength of any BLAST results.

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