similar to: codon usage bias

Dear Colleague, Happy New Year! As we know, codon preference among different species could be dramatically different. To enhance the expression level of a foreign protein in a particular expression system (E.coli, Yeast, Insect, or Mammalian cell), it is very important to adjust the codon frequency of the foreign protein to match that of the host expression system. One classic example is GFP

Dear Colleague, Happy New Year! As we know, codon preference among different species could be dramatically different. To enhance the expression level of a foreign protein in a particular expression system (E.coli, Yeast, Insect, or Mammalian cell), it is very important to adjust the codon frequency of the foreign protein to match that of the host expression system. One classic example is GFP

Hey guys, Does anyone have an example of a REALLY simple shell script in R. Basically i want to run this command: library(MASS) wilcox.test(list1,list2,paired=TRUE,alternative=c("greater"),correct=TRUE,exact=FALSE) in a shell script something like this: #!/bin/bash R library(MASS) for i in *.out do wilcox.test($i,${i/out}.out2,paired=TRUE) >> $i.out done that i can run on a

Hey guys, can anyone help? i have a sample table: >table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1", "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2", "codon3"))) >table codon1 codon2 codon3 gene1 4.0 7

SocketError in EmailController#correspond getaddrinfo: no address associated with hostname. Please see above, these are the errors i get when i try to email a user on my networking site. Can you help please. Actionmailer address = smtp.vodafone.ie Below is code used for the email controller in apps/controllers/email_controller.rb There doesnt seem to be any code missing. Can someone help with

Hey guys, I'd really appreciate any help. I have a multivariate analysis done, the output of which is: > GraphData <-read.table("eigen.coa") > GraphData V1 V2 V3 V4 1 1 0.371970 0.8552 0.8552 2 2 0.061785 0.1420 0.9972 3 3 0.001211 0.0028 1.0000 4 4 0.000000 0.0000 1.0000 > summary(GraphData) V1 V2 V3

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPlot() is now available.

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPlot() is now available.

Hi I would like to plot the variation of some mean values with time, and have the standard deviation around the mean shaded on the plot. I could not find a way to have the shaded area on the curve with the default R commands, do I need a special package to do that? Or any idea of a way with the default R commands? Many thanks Thomas -- Thomas Loridan King's College email: thomas.loridan

Hey guys, Can anyone help? I did a correspondance analysis and made a plot. I also have a specific list of nodes that i want to find in my plot and want to either color the nodes that appear in my list differently, or put some kind of border around that group of nodes... Would anyone know how to do this? Also, would this post be more relevant here or in the bioconductor forum? -- View this

Hey guys, if i do a correspondance analysis, e.g.: table <- structure(c(4, 7, 0.2, 3, .1, 7, 222, 3, 10, 5, 11, 8, 8, 10, 7), .Dim = c(5L, 3L), .Dimnames = list(c("gene1", "gene2", "gene3", "gene4", "gene5"), c("codon1", "codon2", "codon3"))) Library(ca) plot(ca(table)) is there a way that i can see

 Sir,  I am a student in biostat and bioinformatics.  I am interested to use R for my research work related to codon usage analysis.This software was used in a publication entitled " Online synonymous codon usage analyses with the ade4 and seqinR packages" and a weblink  http://pbil.univ-lyon1.fr/datasets/charif04/ was given for readers to use the program. Now  I would like to use the

Hello I have two lists of numbers, each list is ~800 numbers long. I want to know if the two lists are significantly different from each other. Could anyone suggest what library in R to use? I think maybe the mann-whitney test, as it is not parametric, but i am unsure if it is suitable as my list of items are so long.So i am unsure which library would suit best. Aaral. [[alternative HTML

Hi Dave, ----- Mail original ----- > Changes since v1: [...] > diff --git a/drm/nouveau/nouveau_vga.c b/drm/nouveau/nouveau_vga.c > index 9a6328f..7b13804 100644 > --- a/drm/nouveau/nouveau_vga.c > +++ b/drm/nouveau/nouveau_vga.c > @@ -36,7 +36,7 @@ nouveau_switcheroo_set_state(struct pci_dev *pdev, > { > struct drm_device *dev = pci_get_drvdata(pdev); > > - if

Hi useR's, I am resending this request since I got no response for my last post and I am new to the list so pardon me if I am violating the protocol. I am trying to use the "Kernlab" package for training and prediction using SVM's. I am getting the following error when I am trying to use the predict function: > predictSvm = predict(modelforSVM, testSeq); Error in

Hi LLVMers, For your interest, I recently came across the ccg library "dynamic code generation for C and C++". --> http://www-sor.inria.fr/projects/vvm/realizations/ccg/ccg.html It seems to share some points with LLVM. -- Sébastien

Dear helpers, When I use the function cgt of library Rwave, the time axis of the plot is always on the [0,1] scale regardless of the original time. This happedn when I tried to reproduce some pictures of "Practical Time-Frequency Analysis", e.g. Figure 3.5 and 3.6 using the codes provided in the book. But the figures of the book display the real sampling time using the same codes.

Hello, I have a strange h323 issue. After executing command "Dial("SIP/333-0d1dfe00", "H323/361737052390920 at ccg|5|tT")" at Oct 18 22:32:23. Meanwile I have sniffing traffic on port 1720. The call was established just at Oct 18 22:33:03 (New H.323 Connection created.) and also packet sniffer grabs the h323 invites at this time also. So my question is what

Hello. I'm having trouble installing rgl. I have a theory as to the problem. First, the error message and session info. > install.packages("rgl") trying URL 'http://probability.ca/cran/src/contrib/rgl_0.81.tar.gz' Content type 'application/x-gzip' length 1636939 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb *

Buenas, Me encuentro con el mismo problema, de que me dice que el argumento del if no es un "valor ausente donde TRUE/FALSE es necesario" Este es mi codigo de pruebas. readseq <- "aaaaaaaaaaa", "aaa", "aa") auxiliar <- count(readseq[j],i+2) aux_a <- auxiliar["listaa"] if(aux_a > 0){ matrizgraf3[i][k] = matrizgraf3[i][k] + 1 listaa