similar to: Align two protein sequences using BLAST

Dear R users, i try to produce the fold change versus fold change plot where i have the values for x and y ranging from 0.01 to 100. So i start with plot(x,y,xlim=c(0.01,100),ylim=c(0.01,100), axes=F). Then i would like both axes to have tick marks as c(0.01,0.1,1,10,100) but they should appear equidistant. How should i manage this? Thank you for your help, Alla.

Dear R users, i try to use function dmvnorm(x, mean, sigma, log=FALSE) from R package mvtnorm to calculate the probability of x under the multivariate normal distribution with mean equal to mean and covariance matrix sigma. I become the following Error in solve.default(cov, ...) : system is computationally singular: reciprocal condition number = 1.81093e-19 What could be the reason of it?

Hi, I have a glusterfs volume replicated on three nodes. I am planing to use the volume as storage for vMware ESXi machines using NFS. The reason for using tree nodes is to be able to configure Quorum and avoid split-brains. However, during my initial testing when intentionally and gracefully restart the node "ned", a split-brain/self-heal error occurred. The log on "todd"

Dear R users, I'm running R version 2.10.1. I tried installing the Cairo package and I got the following message: * installing *source* package ?Cairo? ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for

Hi, could you please tell me if there is a way, to make dovecot notify my mail client of new messages in inbox subfolders? I'm using fdm to fetch mails into maildir and proper subfolders. So far, when idleing mozilla gets a notification when new message arrives in INBOX, but if mail is fetched into other folder I have to click on it to see if there is a new message. I've checked

Hola Carlos. Muchas gracias. No es exactamente lo que estoy buscando (sería genial ver que alguien tiene un paquete con la prueba de Nam-D'Agostino) pero puedo aprovechar algo de código. Encontré alguna referencia al test de Gronnesby&Borgan en el paquete stcoxgof de Stata, pero estoy torpe para encontrar algo hecho en R (y me extraña que no haya nada) Un saludo, Miguel. De: Carlos

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

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Fri, 15 Dec 2017, Bill Shirley wrote: > This is what I use.? Notice the comma: > require "fileinto"; > if header :contains "X-Spam-Status" "Yes," { > ? fileinto "SystemFolders.SuspectedSpam"; > ? stop; > } I would even add the space: if header :contains "X-Spam-Status"

hi, recently i discovered the functionability summary.formula, awesome! from the help page i understand that method=reverse allows to summarize all variables on the right hand side of formula (the help page on line 229 wrongly refers to the left? hand side variables) in categories which are determined by a single left hand side variable. my problem is that the argument fun seems not to be

hello if there is a package can do blast in R? [[alternative HTML version deleted]]

Dear all, A new task view on survival analysis is now online. It attempts to deal with all the R-packages that permit to analyze time-to-event data. Any comments or suggestions to improve the task view are very welcome. Best regards, Arthur Allignol Freiburg Center for Data Analysis and Modeling, Freiburg University, Germany

I experienced the following problem with R 1.3.0 which is probably a bug. The program hangs-up if 1.) a coordinate of segments is outside the ploting region and 2.) the option log="x" is used. ## ## works fine ## plot(1,1, xlim=c(0.5, 2), ylim=c(0.5, 2)) segments(0.5 , 1.2, 1, 0.6) segments(0.25, 1.2, 1, 0.6) segments(1 , 1.2, 1, 0.6) ## ## hang-up ## plot(1,1, xlim=c(0.5, 2),

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

Hi, I read in the Asterisk Whitepaper, that you can run two cloned servers, one as a primary, one as a backup, and have them automatically failover to the other unit when it crashes, or when you need to restart it. The primary application of course, would be ensuring calls can be made when frequent updates are being handled, or when an update must be restarted on a busy network. The term

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

Anyone have any experience with MpiBlast and Lustre. We have MpiBlast-1.4.0-pio and lustre-1.6.3 and we are seeing some pretty poor performance with most of the mpiblast threads spending 20% to 50% of their time in disk wait. We have the genbank nt database split into 24 fragments (one for each of our OSTs, 3 per OSS). The individual fragments are not striped due to the

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

Hi All, I have use the BLAST program provided by NCBI to compare large databases and have generated a lot of output in one long text file. I was looking for a way to parse out the results in a nice way so that it could be easily visualized. I was thinking of trying to write something in R, but I wanted to check in with the help group to make sure I am not re-inventing the wheel. Any help

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

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