Part V: Comparing FASTA and BLAST and SSEARCH

Instructions:

1. Go to https://www.ebi.ac.uk/Tools/sss/

2. You will do a nucleotide search using the STS mRNA from the previous step using

FASTA, BLAST, and SSEARCH.

3. Leave the database as the default setting.

4. Select FASTA as your program, select more options, and set the following parameters:

5. Match/Mismatch: +3/-2

6. Gap Open: -5

7. Gap Extend: -2

8. Run the search and note the name, score, and e-value of the best hit.

9. Repeat this for BLAST and SSEARCH.

Questions:

1. What were your best hits for each of the different search algorithms?

2. Were they different and if so why?

3. Why was it necessary to set the parameters as described above before running the

searches?