similar to: 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 question urgent. 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

may some one please help me to sort this out, i am trying to writ a R code for calculating the frequencies of the amino acids in 9 different sequences, i want the code to read the sequence from external text file, i used the following code to do so: x<-read.table("sequence.txt",header=FALSE) then i defined an array for 20 amino acids as following:

Dear R developers I am currently working on the seqinR package. The seqinR package allows a remote access to biological databases via a socket connection. We are using the functions socketConnection, writeLines and readLines to open the socket, send request to the server and receive response from the server respectively. Recently, a new function implemented in the socket server allows

Dear all, I am a R beginner, and I am looking for a way to do the same thing for all levels of a column in a table. Basically, I have a bunch of protein sequences composed of different amino acid residues, and each residue is represented by an uppercase letter. I want to calculate the ratio of different amino acid residues at each position of the proteins. Here is an example table: Proteins

All Is there a package or library that will, given a nucleotide sequence 1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law) 2. calculate molecular weight 3. return it's complementary sequence I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids. Any pointers, etc. would be

library(sos) (mp <- findFn('{molecular properties}')) ????? ** found 7 matches in 4 packages and opened two web pages in my default browser with (a) the 7 matches and (b) the 4 packages. The first function was something for amino acids, like you suggested.? Two others returned compound and substance information from PubChem. ????? Does this help? ????? Spencer On

Dear all, I have a data which is in text file and i would like to import the data to R. From the manual, i?ve found the read.table command function is the most appropriate but when i wrote the command an error had occur. It say ?Error in read.table"C:/Users/user/Documents/cfa-1.txt", header = T, sep = "\t",skip=10) :more columns than column names?. Please help me with this as

I have also posted this on IRC. I have a linux host running stock RHEL 5.4 Samba 3.0.33-3.15. The host acts both as a Samba server and does a CIFS mount of that same share. The reason for doing this is so that programs running on the Linux host have the same case insensitive view as the Windows clients. I have nocase set in the relevant line in /etc/fstab I have case sensitive = No set in the

hello every one, How to function more than one loop in R? I have the following problem to be solved with the a method of three loops, can you help me please? The data is attached with this message. The data is composed of two parts, cleaved (denoted by ?cleaved?) and non cleaved (denoted by ?noncleaved?). ? to access to the ith peptide, you can use X$Peptide[i] ? to access to the ith label,

... In addition, you may wish to also post on the Bioconductor list for this sort of thing. -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Thu, May 3, 2018 at 12:58 AM, Spencer Graves <spencer.graves at effectivedefense.org>

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

Hello all: I have a protein sequence alignment in a data frame (align1, 72 x 236), where each row is a protein and each column a site in the alignment. AA is vector of amino acid symbols plus "-" (gap). I can calculate amino acid frequencies at each site by: >align1.F <- matrix(0,nrow=22,ncol=236,dimnames=list(AA,seq(1:236))) >for(i in 1:236) >

Hello: I am attempting to use R to analyze amino acid frequencies in aligned protein sequences and need some help. So far, I have imported my sequence alignment into a data frame (lets call it "alignment") with each site in one column, so that I have a data frame consisting of columns of letters (the 21 amino acid symbols plus "-") with row names being the corresponding

Hi all, I am learning R by "doing". And this is my first post. I want to use R: 1- to fetch a DNA sequence from a databank (see bellow) and 2- store it as FASTA file. The problem: neither an error is prompted nor the fasta file is created. Testing the code (see bellow), I notice that everything works until the *"write.dna" *command - which is not creating the fasta file.

Hi all, when I type this: ruby script/plugin install svn://projects.jkraemer.net/acts_as_ferret/tags/stable/acts_as_ferret from my rails project the plugin is not getting installed, its simply going back to my rails application. I don''t find the plugin in the vendor/plugin directory I am using Instant Rails for your information. Could anyone please let me know whats going wrong...

Hi, I would really like to have a way to split long string literals across multiple lines in R. Currently, if a string literal spans multiple lines, there is no way to inhibit the introduction of newline characters: > "aaa + bbb" [1] "aaa\nbbb" If a line ends with a backslash, it is just ignored: > "aaa\ + bbb" [1] "aaa\nbbb" We could use

Dear users, In my psychometric test i have applied logistic regression on my data. My data consists of 50 predictors (22 continuous and 28 categorical) plus a binary response. Using glm(), stepAIC() i didn't get satisfactory result as misclassification rate is too high. I think categorical variables are responsible for this debacle. Some of them have more than 6 level (one has 10 level).

Dear all, I am trying to make a series of waffle plot-like figures for my data to visualize the ratios of amino acid residues at each position. For each one of 37 positions, there may be one to four different amino acid residues. So the data consist of the positions, what residues are there, and the ratios of residues. The ratios of residues at a position add up to 100, or close to 100 (more on

hi i am new to R language. I want to use aaMI package which calculates the amino acid mutual interaction for a given protein sequence. I had installed the package but when i run the program it gives me the error could not find function "aaMI". can anyone tell me what might be the problem.. -- View this message in context: http://www.nabble.com/aaMI-tp14915744p14915744.html Sent from

I have following codes for ggplots. The legends are given in the plot do not match with the values specified in the codes given below. Your helps highly appreciated. Greg library(ggplot2) p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+ theme_bw() +theme(panel.border=element_blank()) + geom_point(size=3) p2<-p+scale_color_manual(name="Super.Pathway",