Cbcb:Pop-Lab:Niranjan-Report: Difference between revisions
| Line 9: | Line 9: | ||
===Papers Read=== | ===Papers Read=== | ||
# [[Media:rabadan2007.pdf|Non-random reassortment in human influenza A viruses]] | # [[Media:rabadan2007.pdf|Non-random reassortment in human influenza A viruses]]. R. Rabadan, A.J. Levine and M. Krasnitz. | ||
R. Rabadan, A.J. Levine and M. Krasnitz. | |||
The basic idea in this paper is that if you assume constant | The basic idea in this paper is that if you assume constant | ||
rate of mutational drift in different segments of the same strain (an | rate of mutational drift in different segments of the same strain (an | ||
assumption that seems to be true on a coarse level for some segments, but | assumption that seems to be true on a coarse level for some segments, but | ||
not for others) then given two non-reassorted strains the nucleotide | not for others), then given two non-reassorted strains, the nucleotide | ||
differences between their NA segments should be roughly proportional to | differences between their NA segments should be roughly proportional to | ||
that from the HA segments and they use that as a test to identify putative | that from the HA segments and they use that as a test to identify putative | ||
| Line 22: | Line 21: | ||
seem to make no attempt to figure out if a set of taxa have reassorted | seem to make no attempt to figure out if a set of taxa have reassorted | ||
based on a common event. Finally, there is no evaluation of the capability | based on a common event. Finally, there is no evaluation of the capability | ||
of this method | of this method - just a list of results which seem to clearly miss the | ||
reassortments we already know of | reassortments we already know of. In fact, in the abstract, they make the | ||
find all the reassortments from earlier works | claim that they find all the reassortments from earlier works. | ||
Revision as of 15:22, 16 February 2009
March 2nd, 2009
Tasks
- Made more updates to my webpage
- Started making a presentation for my job talk
- Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.
Papers Read
- Non-random reassortment in human influenza A viruses. R. Rabadan, A.J. Levine and M. Krasnitz.
The basic idea in this paper is that if you assume constant rate of mutational drift in different segments of the same strain (an assumption that seems to be true on a coarse level for some segments, but not for others), then given two non-reassorted strains, the nucleotide differences between their NA segments should be roughly proportional to that from the HA segments and they use that as a test to identify putative reassortments. They use a vaguely described idea to figure out which combination of segments have reassorted (probably done manually) and they seem to make no attempt to figure out if a set of taxa have reassorted based on a common event. Finally, there is no evaluation of the capability of this method - just a list of results which seem to clearly miss the reassortments we already know of. In fact, in the abstract, they make the claim that they find all the reassortments from earlier works.