tag:blogger.com,1999:blog-32079676.post115521799940025858..comments2024-02-13T21:22:02.522-08:00Comments on RRResearch: How DNA functions constrain USS locationsRosie Redfieldhttp://www.blogger.com/profile/06807912674127645263noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-32079676.post-1155231612318513552006-08-10T10:40:00.000-07:002006-08-10T10:40:00.000-07:00I keep coming back to preferred codon usage in Hi,...I keep coming back to preferred codon usage in Hi, but in no clear way, and I need to do a lot more reading! But I wonder if the perfect USS can be thought of as an optimum in that it doesn't code for any particularly rare amino acids in any of its possible frames. Also, is it right to think of the perfect USS as being at the top of a finess peak, and maybe a wonderful 3-off on the next peak (no rare amino acids in any frame etc) has little chance of arising because of the combined effects of receptor preference and deleterious one-off and two-off changes.LindsayAWilsonhttps://www.blogger.com/profile/09666151957693399667noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-1155230551892421242006-08-10T10:22:00.000-07:002006-08-10T10:22:00.000-07:00I spoke with someone yesterday about using WestGri...I spoke with someone yesterday about using WestGrid. Apparently it is not possible (?) to have the arguments given by the user at the beginning (such as genome size, GC content, etc). So I think I should write these in the code. This will also make automation much easier. We can use several different mutation rates, converstion rates, and so on. I guess we should talk more about this, and the definition of equilibrium.90% microbehttps://www.blogger.com/profile/10288595333674587852noreply@blogger.com