Cbcb:Pop-Lab:Niranjan-Report: Difference between revisions
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Report for March 2nd, 2009 | Report for March 2nd, 2009 | ||
[[Tasks]] | |||
1) Made more updates to my webpage | |||
2) Started making a presentation for my job talk | |||
3) Assisted Carl in writing a grant proposal to extend on our | |||
work on reassortments in the Flu genome. | |||
[[Papers Read]] | |||
1. [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 they make the claim that they | |||
find all the reassortments from earlier works, in the abstract! | |||
Revision as of 15:07, 16 February 2009
Report for March 2nd, 2009
1) Made more updates to my webpage 2) Started making a presentation for my job talk 3) Assisted Carl in writing a grant proposal to extend on our
work on reassortments in the Flu genome.
1. [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 they make the claim that they find all the reassortments from earlier works, in the abstract!