search for: amino

...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$Peptide[i] ? to access to the ith label, you can use X$Label[i] define a set of amino acids using string or other format if you want amino.acid<-"ACDEFGHIKLMNPQRSTVWY" define two matrices with initialised entries, one for cleaved peptides and one for none-cleaved peptides ? matrix(0,AA,mer),where AA is the number of amino acids, and mer is the number of residues detect...

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: AA<-c('A','C','D','E'...

...", "Arginine", "Glutamate", "Glycine", "Serine", "Glucose", "Fructose", "Raffinose", "Glycerol", "Galacglycerol", "Threitol", "Galactinol", "Galactitol") Class<-c("aminos","aminos","aminos","aminos","aminos","sugars","sugars","sugars","glycerols","glycerols","sugar alcohols","sugar alcohols","sugar alcohols") set.seed(5) Ratio<-rnorm(13,...

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 statistics of this string such as how m...

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 Time_zero 1 2 3 4 5 6 7 8 p1 0.0050723 L E Y I I P D A p2 0.0002731 T E...

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) > align1.F[names(summary(align1[[i]])),i] <- (summary(align1[[i]])/length(align1[[i]])) Is there a mo...

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 "-&q...

...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 great. thank you in advance Indr

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 statistics of this string such as how many...

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 2018-05-02 19:17, bbb_aaa at verizon.net wrote: > All > > Is there a package or library that will, given a nucleotide sequence > > 1. calcula...

...e 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", labels=c("Amino Acid", "Cofactors and Vitamins", "Carbohydrate", "Energy", "Lipid", "Peptide", "Nucleotide"), values=c("Amino Acid"="red", "Cofactors and Vitamins"="purple", "Carbohydrate"="d...

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...

Dear mailing list, I'm stuck with a tricky problem here - at least it seems tricky to me, being not really talented in pattern matching and regex matters. I'm analysing amino acid mutations by position and type of mutation. E.g. (fictitious example) in position 92, I can find L92V, L92MV, L92I... L is in this example the wild-type amino-acid, and everything behind the position number is a mutation (single amino acid or mixture). I'm only interested in the mutation i...

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 this soon)*....

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-tp14915744p149157...

...org> wrote: > > 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 2018-05-02 19:17, bbb_aaa at verizon.net wrote: >> >> All >> >> Is there a package or library...

Hi there, I have a large amino acid csv file like this: input.txt: P,LV,Q,Z P,VL,Q,Z P,ML,QL,Z There is a problem with this file, since LV and VL are in fact the same thing. How do I order each element according to alphabetical order so that the desired output would look like: output.txt: P,LV,Q,Z P,LV,Q,Z P,LM,LQ,Z --...

...res of thermophilic adaptation, subcellular localization, proteomic stress response, and microbial diversity. Calculation of the standard Gibbs energies of proteins is based on a published group additivity algorithm and is further supported in this package by the inclusion of data files for the amino acid compositions of selected proteins and of proteins in yeast and E. coli. A paper describing some applications of the package can be found in Geochemical Transactions: http://www.geochemicaltransactions.com/content/9/1/10 The project website highlights many of the example calculations. Ther...

...res of thermophilic adaptation, subcellular localization, proteomic stress response, and microbial diversity. Calculation of the standard Gibbs energies of proteins is based on a published group additivity algorithm and is further supported in this package by the inclusion of data files for the amino acid compositions of selected proteins and of proteins in yeast and E. coli. A paper describing some applications of the package can be found in Geochemical Transactions: http://www.geochemicaltransactions.com/content/9/1/10 The project website highlights many of the example calculations. Ther...