The goal of this exercise is for you to become familiar with Blast searches. You will generate tons of output during this exercise - DO NOT PRINT IT ALL OUT.

1. Use BlastN to compare the sp18 DNA sequence to the non-redundant database. This protein comes from species of the Genus Haliotis. How many significant matches are in the database? How many complete sequences are in the database, and from how many different species (give the species names)?

2. Use BlastX to compare the sp18 DNA sequence to the non-redundant protein database and answer the same questions. What are the E-values for some of the matches, and how do you interpret the scores?

3. Use BlastP to search the sp18 protein sequence against the non-redundant database. How do the E-values compare to the BlastX search, why do you think they are similar or different? Do the search with and without the filter -‚ are there any differences? Do the search with different scoring matrices -‚ are there any differences? If there are differences, why do you think there is a difference? There should be some matches to sperm lysin from the same genus, based on these database searches is sp18 homologous to sperm lysin?

4. Use BlastP to search the sp18 protein sequence against the protein databank database (pdb) of 3D structures. Are there any proteins homologous to sp18 where the 3D structure is known? How does the E-value compare to the same hit as found using BlastP against the nr database? If there is a difference, why do you think there is a difference?

5. Based on your database searches, what is the function of the sp18 protein? You can follow links to the references.

6. Use the lysin protein sequence to perform a protein Psi-Blast search. According to this anlysis, are the lysin and sp18 fertilization proteins homologous? What is the difference between the Psi-Blast and BlastP analysis done above?

7. Find a gene of interest using either the UCSC browser to NCBI Entrez. Perform similar searches with a gene of your own interest. Is there a 3D structure? How many homologues are in the database?

Write a description of what you did during the lab exercise. Address the questions raised above. You can include a few outputs, but DO NOT include all blast outputs. Describe how you interpreted the E-values, the different databases searched, why results are different with different matrices, and why the E-values are different when you use different input parameters (database, matrix, filter).