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Phylogenetics Laboratory

Independent Phylogeny Project



ASSIGNMENT

Independent study on a particular question that can be addressed using DNA sequence data from GenBank.

Use data that are already grouped into sets of related and at least partially aligned sequences.  This is the POPSET section of GenBank.  However, this does not necessarily preclude you from looking for related sequences in GenBank using BLAST.

To access POPSET get into Genbank, click ENTREZ, and click on POPSET which is in the far right of the black bar near the top.

Then you can search POPSET by entering a search word, or number.

Once you submit the search, titles of relevant data sets (groups of DNA sequences) are listed.  These titles are often only partly informative, so you may want to go deeper. To do this, click on the Author's name, and this brings up information on what sequences are there (their length, and how many).  If they are not aligned there will be a note in purple to that effect.

To get more details on the study, click on the accession number of one of these sequences.   This may give you a reference to the study, or it may say something about the particular sequence, etc.

FOR NEXT WEEK

Come up with a half page summary of TWO possible projects, each based on a question that you want to ask of the data.
In this summary include the number of the POPSET that you are thinking of using.
We will discuss these at the next lab.

Also bring your "Fasteners" data set on a diskette in a form suitable for PAUP.

Attached are some examples you may want to scan to get the general idea.
Example POPSETS (with their popset numbers that you can search on):
4406443 - Polymorphism in the horse DQA locus.
5918987 - Which humans colonized Australia and New Guinea.
6579044 - Loss of drug resistance in HIV following cessation of therapy.
7025369 - Rapid evolution of male reproductive genes in the descent of man.
5802203 - Retroviruses in cats and baboons. Are they related?
7288748 - E. coli from different host species
3873254 - Phylogeny of Cryptosporidium parasites in relation to vertebrate hosts.
5764580 - Constructing primate phylogenies using ancient retrovirus sequences.



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