Assignments #1:

1. Do a medline search for papers authored by Gogarten. What are the initials of your instructor?

2. How many paper authored by your instructor do you find in medline (=pubmed)?

3. Select the related papers from the 1989 PNAS publication. How many related articles are linked to this paper?

4. What is the most recent related article among the first 40 related articles?

5. Find the paper by Zimniak L, Dittrich P, Gogarten JP, Kibak H, Taiz L.
How many related protein and DNA links does this paper have?

6. Are these different sequences? How come?

7. If you follow the first protein link (in the article from question number 5), how many related protein sequences do you find related to the protein?

8. If you follow the DNA link in the article, how many related nucleotide sequences do you find related to this nucleotide sequence?

9. Can you explain the difference to question 7?
Assume that you retrieved a protein encoding gene and are looking for related sequences. Would you be better off using the protein or the nucleotide sequence?

10. Use Entrez to find RubisCO (=ribulose bisphosphate carboxylase oxygenase = rbcl ) encoding genes in Archaea. How many archaeal RubisCO homologues can you find in the protein databank?
List the species:
(there are more than three _ it is not easy to formulate a good Boolean search)

Is there an archaeal species that has more than one RBCL gene? (RBCL= ribulose bis phosphate carboxylase large subunit)

***** 11 and 12 will be continued next week *****

11. Using entrez download the protein sequence with PID 2506213.
What type of proteins do you find among the related proteins?

12. Copy the FASTA format of g2506213 onto your computer-s clipboard (not the clipboard of the ncbi page), go to the NCBI blast page and do a gapped blast search (otherwise default options).

Do you obtain any different results (compared to the related proteins in question 11)?