Biodatabases / exercises  Tuesday 20.1.09
Go  to  influenza virus database:
http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
Read about the facilities of the database, then click ?database? and find answers to the following questions.
Send answers to sirkka-liisa.varvio@helsinki.fi during this week. Please, do not send large datasets as answers, just give answers to the questions in a short way, so that I can see that you have performed the work and you seem to know how to work with (this) database.
The window segment / protein defines, for example H/N, for example the famous H5N1 genes, HA= haemaglutinin, NA= neuraminidase.
In the exercises restrict the queries to these segments (HA or NA). 
1.Has the giant anteater (= an animal) been infected by influenza virus (on the basis of sequence database information)? By what type of the virus?
2.Same question concerning seals.
3.Give references to those publications which report sequences found from seals.
4.How many sequences from influenza A exist  in the database concerning European people? 
5.Get influenza A sequences from swine from North America. How many there are? 
6.Use the facility ?build a tree? for the swine sequences from Nort America. This means rough phylogenetic tree construction, use neighbor joining, don?t  pay any attention to different options, because this is not a course for phylogenetic inference??just use the tree as a facility to visualize the data).   When you get the tree, what can you see, describe shortly. For example, what is the the sequence at the ?top? of the tree and what is at the  ?bottom??
7. Get influenza A sequences from cat from Europe. 
 Use the facility ?do multiple alignment?.
 From the alignment, find out:  at how many amino acid sites there are   differences between the different sequences.
Some of the sequences have been published, i.e. there are links to articles:
What are the articles?