1) Michael Crichton's fantasy about cloning dinosaurs, Jurassic Park contains a putative dinosaur DNA sequence. Use nucleotide-nucleotide BLAST against the default nucleotide database to identify the real source of the following sequence:

2) Mark Boguski of the NBCI noticed this and supplied Crichton with a better sequence for the sequel, The Lost World. Identify the most likely source of this sequence using nucleotide-nucleotide BLAST. Mark imbedded his name in the sequence he provided. To see Mark's name use the translating BLAST (blastx) page the sequence below. (Look for MARK WAS HERE NIH).

3) The C. elegans gene SMA-4 is a member of the dwarfins gene family, which play a role in TGF-mediated signal transduction. In order to identify potential homologs in other species, use the protein-protein blast page to perform search against the non redundant protein database (nr) using SMA-4 (accession number P45897) as the query sequence. Find all chicken (Gallus gallus) proteins that are similar to SMA-4. (Use the Tax Blast link at the upper left of the graphic to help in finding the chicken proteins.) Now run the search again and restrict to chicken proteins through the Entrez query advanced option. What proteins are found? Compare the Expectation values of these hits to the same hits found against nr with no organism restriction. Why are the E values different for the same scores and alignments?

4) The human fragile histidine triad protein (FHIT) (SWISS-PROT: P49789) has been shown to be structurally homologous to galactose-1-phosphate uridylyltransferase. However this relationship is not apparent in an ordinary BLAST search. Perform a protein-protein blast search against the swissprot database with P49789 and search your results for galactose-1-phosphate uridylyltransferases.

5) Find the unannotated genomic scaffold for Drosophila melanogaster, AE003584, using Entrez nucleotides. Display protein links to see the predicted proteins for this scaffold. Use the CDD search to identify conserved domains present in the tenth predicted protein (gi: 7295996) and suggest a potential function for this hypothetical protein.

6) As GenBank grows so does the number of chance occurrences of amino acid motifs that spell out words or people's names in single letter amino acid codes. One such name motif is ELVIS. Find the number of occurrences of ELVIS in the protein 'nr' database. To get any hits at all, you will have to adjust several of the advanced BLAST parameters including the Expect value, Word size and Score Matrix. Adjust some of these in the "Other advanced options" box. Options are entered command line style. For example, typing

	-e 10000

sets the Expect value cut-off to 10000. See the BLAST "Frequently Asked Questions" linked on the left side bar of the BLAST page on "How do I perform a similarity search with a short peptide/nucleotide sequence?" for more information. We now have a page with presets optimized to find short nearly exact matches. You can cheat and run the search on this page to see the correct parameters to use.