Assignments #1:

    Answer
1 Do a medline search for papers authored by Gogarten.
Can you guess the initials of your instructor?		  
2 Select the related papers from the 1989 publication in the proceedings of the National Academy.
How many related articles are linked to this paper?		  
3

Sort the papers from #2 according to date.
When was the paper is on top of the sorted list published?

 
4 How many related protein sequences do you find in all of these papers taken together? (use the pulldown menu on top, without any check marks)  
5 Find the paper co-authored by Senejani and Gogarten. What was the topic of the paper?  
6

Display the abstract of this paper and click on the book link (on top right of abstract). Items in the abstract that are covered in the reference book turn into hyperlinks. If you need more information on any of the items follow these links.
Follow the one but last link (Phylogenetic), select "Molecular Biology of the Cell" and click on the first link.
According to the diagram, which bacteria gave rise to the plastids of red and green algae?
Do you believe this?

 
7 For this question it is advisable to use the index function. Try to find RubisCO (=ribulose bisphosphate carboxylase oxygenase = rbcl = ribulose bis phosphate carboxylase large subunit) 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)		  
8 In 7, did you find any archaeal species that have more than one RBCL gene?  
9 Using entrez find the sequence with gi number (gi="gene identification" number) 9502269.
What is the accession number of this sequence?
What is the version number?
What is the difference between these numbers? (Check the link in the lecture notes).		  
10 How many related nucleotide sequences does this sequence have?  
11 To what domain, kingdom and family does Thermoplasma belong? (Use the Taxonomy link)  
12 How many protein sequences are available for Thermoplasma acidophilum, how many are available for the genus Thermoplasma? (In the taxonomy browser go to Thermoplasma and check protein in the header)  
13 Go to the protein sequences linked to GI:9502269. How many related sequences does this protein sequence have? (Why are there so many more related proteins than nucleotide sequences?)
Are the first three of the related sequences different form one another?
What type of sequences are listed on page 10, 30?		  
14 Check the little box in front of sequence 1, 20, 41 and 45. Copy the entries to your NCBI clipboard using the ClpAdd button. Go to the NCBI-clipboard and select FASTA in the pull-down menu and then click the display button. What does change/happen, when you click the TEXT button?  
15 Go back to protein sequence PID 9502270. Select Blink on the top right above the entry. How many sequence entries are listed?  
16 What happens when you click on common tree?
Place a check mark in the tree infront of archaea and click the choose button. 		 
17 Click on the conserved domain search button. How many conserved domains do you retrieve? Which of these does not point towards the same type of function? What is a possible explanation?