search for: nucleotide

Dear all: I have a character object x with ' (single-quote) character. x <- c('"hydrolase activity","actin binding","3',5'-cyclic-nucleotide phosphodiesterase activity") I want to write a function that will identify ' and replaces with \' myf <- function(term){ if (grep("'",term)) { sub("'","\'",term)} } > myf(x) [1] "hydrolase activity" [2] "actin binding&q...

The myoglobin sequence, with reference number NM_005368 in Gen bank, has the following frequencies of DNA nucleotides: A C G T 237 278 309 242 Do these data provide sufficient evidence, at the 1% level of significance, that the DNA nucleotides have an unequal distribution, that is the DNA nucleotides are not evenly utilised? Clearly state your hypothesis, test statistic and conclusion. Justify your conc...

Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd

Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd [[alternative HTML version deleted]]

Hi, I am very new to R and wanted to know if there is a package that, given very long nucleotide sequences, searches and identifies short (7-10nt) motifs.. I would like to look for enrichment of certain motifs in genomic sequences. I tried using MEME (not an R package, I know), but the online version only allows sequences up to MAX 60000 nucleotides, and that's too short for my needs...

Hello, I'm struggling with understanding the output on the ancestral.pars() command from the phangorn package, I'm new to doing phylogenetic analyses using R. I used it on nucleotide data, and it works fine, I'm just not sure how to read the output. The output is phyDat class, and outputs a matrix for each node/leaf in the tree. I figured out that the matrix columns represent the four nucleotide states a, c, g, t, but what I'm unclear about is what the rows represent,...

Hi, It might be a trivial question but I just wonder if you could advise good theoretical tutorials, reviews on NGS (different platforms) quality control like nucleotides quality by cycle, nucleotides frequency by cycle, GC content and distribution, K-mer frequency by cycle as well as quality control after alignment and mapping. Look forward to your reply, Carol [[alternative HTML version deleted]]

...ay))+ 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"="darkgreen", "Energy"="orange", "Lipid"="darkblue", "Peptide"="darkred", "N...

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...

.... o A new function rearranged.oriloc() is available. This method, based on oriloc(), can be used to detect the effect of the replication mechanism on DNA base composition asymmetry, in prokaryotic chromosomes. o New function extract.breakpoints(), used to extract breakpoints in rearranged nucleotide skews. This function uses the segmented package to define the position of the breakpoints. o New function draw.rearranged.oriloc() available, to plot nucleotide skews on artificially rearranged prokaryotic chromosomes. o New function gbk2g2.euk() available. Similarly to gbk2g2(), this functio...

.... o A new function rearranged.oriloc() is available. This method, based on oriloc(), can be used to detect the effect of the replication mechanism on DNA base composition asymmetry, in prokaryotic chromosomes. o New function extract.breakpoints(), used to extract breakpoints in rearranged nucleotide skews. This function uses the segmented package to define the position of the breakpoints. o New function draw.rearranged.oriloc() available, to plot nucleotide skews on artificially rearranged prokaryotic chromosomes. o New function gbk2g2.euk() available. Similarly to gbk2g2(), this functio...

...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. 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...

The new package RFLPtools is available on CRAN. RFLPtools provides analysis functions for DNA fragment molecular weights (e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities. It aims mainly at the identification of similar or identical fragment patterns to evaluate the amount of different genotypes gained from environmental samples during diversity studies and at further analysis of similarities of nucleotide sequences derived from pairwise seq...

The new package RFLPtools is available on CRAN. RFLPtools provides analysis functions for DNA fragment molecular weights (e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities. It aims mainly at the identification of similar or identical fragment patterns to evaluate the amount of different genotypes gained from environmental samples during diversity studies and at further analysis of similarities of nucleotide sequences derived from pairwise seq...

...sted Marshmallows" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-mingw32/x64 (64-bit) below is the part that works ################################################################################ # The following lines create a string of nucleotides and uses a for loop to create multiple strings. # random.string replicate something based on rs sampling criteria. random.string <- rep(NA, rs<-sample(3:18,1,replace = TRUE)) # The randomizeString function uses members of DNAnucleotides list to sample 3 at a time # placing the results in...

Dear list, This question is about Hidden Markov Model. Given a transition matrix, an emission matrix and a sequence of observed symbols (actually, nucleotide sequences, A, T, C and G), I hope to predict the sequence of state by Viterbi algorithm. I searched R repository for related packages. msm package has function viterbi.msm (as well as very good document), but it only works for continuous-time condition. Other two HMM related packages, hmm.discnp...

...st = plant.height, upper = upper) library(latticeExtra) segplot(reorder(genotype, est) ~ lower + upper, data = x, draw.bands = FALSE, centers = est, segments.fun = panel.arrows, ends = "both", angle = 90, length = 0, par.settings = simpleTheme(pch = 19, col = 1), xlab = expression("nucleotide diversity " %+-% " sd"), panel = function(x, y, z, ...) { panel.abline(h = z, col = "grey", lty = "dashed") panel.abline(v = 14.20, col = "grey") panel.segplot(x, y, z, ...)}) -- View this message in context: http://r.789695.n4.nabble.com/reorder-...

...; [1,] 35838396 36151202 312806 > > [2,] 35838674 35838584 -90 > > [3,] 36003908 35838674 -165234 > > [4,] 36004090 36003908 -182 > > [5,] 36150188 36003992 -146196 > > > > Row 1 is start/end and rows 2 through 5 are end/start> so you only > want to exclude nucleotides that fall > > between start/end in row 1, ignoring rows 2 through 5 > > which are end/start? Given your sample matrix A, which > > rows do you want to include/exclude? > > > > David C > > > > From: JiangZhengyu [mailto:zhyjiang2006 at hotmail.com] > &gt...

...0.1: Ape provides functions for reading, and plotting phylogenetic trees in parenthetic format (standard Newick format), analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences from GenBank via internet, and several tools such as Mantel's test, computation of minimum spanning tree, or the population parameter theta based on various approaches. Bug reports, comments and suggestions on Ape are welcome. E...

I am inserting a DNA sequence into a plot, and hope to colourize each of the four nucleotide of the DNA sequence with a unique colour i.e., A ("red"), C ("green"), G ("blue", and T ("yellow"). I use the following codes, but the DNA sequence only shows as "red" DNA <- "ACGT" plot(1, xlim = c(0,1), ylim = c(0,1), axes=F, xlab=...