1. Compare the alignment scores obtained with small and large gap penalties in the following example: Go to the LALIGN program on the lalign . This program aligns sequences by a local dynamic programming algorithm and includes end gap penalties. LALIGN produces several different alignments, with no two alignments including a match of the same two sequence positions.

a. What is the default scoring matrix for Blosum 50(25%)? b. Obtain two amino acid sequences in FASTA format: RecA from the bacterium Escherichia coli ( NCBI Reference Sequence: NP_417179.1 ) and RAD51 from yeast (ACCESSION #BAA00913). These proteins have the same function, but have diverged enough that they have become difficult to align. Use LALIGN to align the above sequences with gap penalties of 10 and 2. Note the following (from the top most alignment)

(i) the length (overlap) of the alignment, (ii) the % identity, the % similarity and (iii) the scores (waterman-Eggert and bits) of the alignment

c. How many gaps are in the yeast proteins alignment? d. Repeat with gap penalties of 8 and 2 and note the features of the new alignment.

e. How many gaps are now in the yeast proteins alignment? f. Which looks more like a local alignment and which looks like a global alignment (look at gaps and identity)?

2. Repeat question one using the Align two or more sequences feature (use blastp for protein) on the NCBI server.

a. Click Search Summary. What are the default gap opening and gap extension penalties (GAP costs)? b. Which substitution matrix is used? Is this the same one LALIGN uses? c. What is the percent identity of the alignment? d. What is the percent similarity (positives)? e. Explain the significance of the letters and + signs between the sequences.

3. Find the two protein sequences with accession numbers NP_057849 and P10266.

a. From what species are these sequences? b. Perform blastp pairwise alignment with one of the two proteins using the default scoring parameters. Then change the substitution matrix and record all of the results.