1. Apply the Needleman-Wunsch algorithm to the following sequences

1: ATCGATC

2: GATCATT

        (a) Calculate the dynamic programming matrix.

(b) What is the score of the alignment?

(c) What is the optimal alignment?

(c) How would you modify the Needleman-Wunsch algorithm to detect the best overlap between two sequences (semi-global alignment). Note that this amounts to ignoring gaps at the extremities of the alignment.

2. Download the the files some-pre-let-7.fa and tRNAs.fa 

(a) Use ClustalOmega to align the let-7 sequences using the RNA option

(b) Use LocARNA to fold and align the let-7 sequences.

(c) Is the structural alignment useful in this case?

(d) Repeat the previous steps using the tRNA sequences.

(e) Is the structural alignment useful in this case?

3. Download the fasta file containing the upstream region of several bacterial genes known to be regulated by the AbgR TF

        (a) Use ClustalOmega to align the sequences

        (b) Is it useful to identify common motifs?

        (c) Use the MUSA motif finder located in your virtual machine.

        (d) Use MEME selecting ‘any number of repetitions’ and ‘search given strand only’.

        (e) Compare the results.