Displaying 20 results from an estimated 100 matches similar to: "Boost Protein Expression by Codon Optimization"
2004 Jan 06
0
Boost Protein Expression by Codon Optimization
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
2012 Feb 29
1
codon usage bias
Hey guys, I have what i think is a really simple problem :(
I installed the seqinr library. I want to do an RSCU analysis.
But i can't get it to work in even the simplest case. for example, if i have
a string read in:
> newdata5
$testseq
[1] "agtgagatgatagatagatagatagatagatagatagaccccccagata"
and then i perform an RSCU analysis on it...
>
2012 Apr 09
0
Help using R 2.14.2
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
2010 Apr 22
1
cell-based high-throughput chemical compound screens package?
Hi
I'm looking for a package to perform quality control, normalization and analysis of high throughput cell-base chemical screens. I know that the cellHTS2 package provides this for siRNA screens.
Does anybody know if something like what I'm looking for exists?
Thank you!
Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova,
2010 Aug 20
1
error heatmap and stack overflow
Hello,
Im trying to create a heatmap with a dataset (38 x 15037) but get the
error below:
Error: protect(): protection stack overflow
Execution halted
or
Error: C stack usage is too close to the limit
Execution halted
I tried to increase the stack size by changing:
extern uintptr_t R_CStackLimit
but my systems manager said that R by default uses all the memory
available to it from the
2010 Mar 17
0
Preclinical Statistician
The right candidate will work closely with neuroscientists seeking to
discover new medicines to treat Alzheimer?s disease, bipolar illness,
schizophrenia and autism. He/she will be involved in the design and
analysis of preclinical experiments covering all aspects of drug
discovery from disease target identification through animal model
development and demonstration of proof of concept. The
2011 May 24
1
seeking help on using LARS package
Hi,
I am writing to seek some guidance regarding using Lasso regression with the
R package LARS. I have introductory statistics background but I am trying to
learn more. Right now I am trying to duplicate the results in a paper for
shRNA prediction "An accurate and interpretable model for siRNA efficacy
prediction, Jean-Philippe Vert et. al, Bioinformatics" for a Bioinformatics
project
2010 May 18
1
GUI commands to call for a protein from protein data bank
What I am trying to do is use GUI function, traitr, and to call for a pdb
file and save it and then display it. I want to call for it by taking it
from the user and then displaying it on the screen. I am having problems
with that. The line pdb <- read.pdb(""ProteinCode) where proteincode should
be the name of the protein, for example 1ly2, but it always ends up being
protein. My
2005 Aug 05
0
Cluster analysis of protein time series
Hello!!!
I have a question about clustering. I'll present my problem first.
I have a simulation of a protein trayectory (a file with a time series
of protein 3D-coordinates), from it I can calculate the Root Mean
Square desviation (RMSD) beetween any pair of structures in the
trayectory, which is a rough idea of 3D similarity beetween them. If
for every conformation (trayectory frame) I
2010 Jan 05
2
Align two protein sequences using BLAST
Dear R users,
I would like to align two protein sequences using BLAST
(bl2seq). The question is whether this programm have been
implemented in R.
Thank you for your help,
Alla.
2011 Mar 22
1
Best HMM package to generate random (protein) sequences?
Dear All,
I would like to generate random protein sequences using a HMM model.
Has anybody done that before, or would you have any idea which package
is likely to be best for that?
The important facts are that the HMM will be fitted on ~3 million
sequential observations, with 20 different states (one for each amino
acid). I guess that 2-5 hidden states should be enough, and an order
of 3 would
2011 Sep 13
2
GO & Protein Complex Analysis for Homo sapiens
Dear All,
I need to fetch GO ontologies for Homo sapiens with their mappings to
corresponding Uniprot identifiers. I would be using this information to
compare result from a clustering algorithm with existing protein complexes.
This would be a test to check how the clustering algorithm accurately
captures GO terms with respect to the known protein complexes. Can anyone
suggest a simple workflow
2015 May 28
3
[PATCH v2 8/9] acpi: Add support for Apple Gmux _DMS
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
2010 May 25
4
R eat my data
HI, Dear R community,
My original file has 1932 lines, but when I read into R, it changed to 1068
lines, how comes?
cdu@nuuk:~/operon$ wc -l id_name_gh5.txt
1932 id_name_gh5.txt
> gene_name<-read.table("/home/cdu/operon/id_name_gh5.txt", sep="\t",
skip=0, header=F, fill=T)
> dim(gene_name)
[1] 1068 3
--
Sincerely,
Changbin
--
Changbin Du
DOE Joint Genome
2009 Jan 11
3
Converting Numerical Matrix to List of Strings
Hi all,
Given a matrix:
> mat
[,1] [,2] [,3]
[1,] 0 0 0
[2,] 3 3 3
[3,] 1 1 1
[4,] 2 1 1
How can I convert it to a list of strings:
> desired_output
[1] "aaa" "ttt" "ccc" "gcc"
In principle:
1. Number of Column in matrix = length of string (= 3)
2. Number of Row in matrix = length of vector ( = 4).
3.
2007 Sep 11
4
Questions about the new idmap interface
Hi,
I tried to configure the new idmap interface. Currently without much success.
I have two samba domains, trusting each other. Each PDC using it's own LDAP
server. I tried
idmap domains = DOM1, DOM2
idmap config DOM1:default = yes
idmap config DOM1:backend = ldap
idmap config DOM1:ldap_base_dn = ou=Idmap,dc=dom1,dc=mydomain,dc=de
idmap config
2006 Jun 18
2
analyze amino acid sequence (composition)of proteins
Dear R-helpers:
thank your for your attention.
i am a newer to R and i am doing some protein category classification based on
the amino acid sequence.while i have some questions urgently.
1. any packages for analysis amino acid sequence
2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB"
3. based on "AAABBB",how can i get some
2012 Dec 31
5
[LLVMdev] [lld] Linker script findings.
Hi all, I have been investigating linker scripts and the functionality
needed to support them in lld. I have attached my findings about the
usage of ldscripts. My findings have been collected from:
- Reading all the GNU ld manual sections about linker scripts.
- Looking at the GNU ld and gold source code.
- Digging through a couple embedded programming tutorials.
- Reading through all of the
2008 Nov 28
1
Unable to plot or analyse phylogeny (PR#13345)
Full_Name: Emily Green
Version: 2.8.0 GUI 1.26
OS: MacBrook Pro with 2.5 GHz processor, using Mac OS X 10.5.5
Submission from: (NULL) (144.32.69.137)
I am wanting to correct for phylogeny using a phylogenetic tree of 296 birds
species, which I have constructed myself. The file format is correct and I have
checked its display in Mesquite, which exported the nexus file (I've pasted the
text of
2008 Aug 27
0
Excessive disk activity from browse.dat regeneration
Greetings,
I'm trying to track down and eliminate the sources of excessive disk
activity in an idle system that is resulting in premature hard disk failure.
Access time updates to inodes turned out to be the worst culprit,
triggering writes every 35 seconds or so. Mounting filesystems with the
noatime option fixed that problem.
But not too far behind inode updates is the frequent