similar to: problem with bio3d package

Is it just me, or is the bio3d package no longer available? Is there another way to do a reasonable nucleic acid sequence alignment in R? Thanks, Jonathan [[alternative HTML version deleted]]

Hi everyone,  I am using bio3d package for some sequence analysis because of its nice integrated MUSCLE execution. However, I have been encountering some errors while I was running seqaln function, which calls for installed MUSCLE program. In my case, I stored the MUSCLE program on the desktop with pathway of "./Desktop/muscle/src/muscle". I had no problem running MUSCLE directly from

Hi, As Frank M. Howell noticed (and probably other users), the Windows binaries for DCluster I put in my web page are not working... I have compiled the source code again and know it does. Please, download it again, and sorry for the inconvenience. The URL is http://matheron.uv.es/~virgil/Rpackages/DCluster DCluster is a package that implements some methods for the detection of spatial

Hi, I have just put the source code (and a zip file for Window$ users) of package DCluster in my website: http://matheron.estadi.uv.es/~virgil/Rpackages/DCluster/ DCluster is a package that contains routines for the detection of spatial clusters of diseases (Openshaw's GAM, Besag and Newell, Kulldorff and Nagarwalla, Stone's Test and others). A full description can be found here:

https://bugzilla.samba.org/show_bug.cgi?id=5963 Summary: rsync fails with errors that make no sense... Product: rsync Version: 3.0.4 Platform: x86 OS/Version: Linux Status: NEW Severity: major Priority: P3 Component: core AssignedTo: wayned@samba.org ReportedBy: crhea@mayo.edu

I suspect you meant WD <- "~/Documents/Scripting/R_Studio/Sequences/" but I am entirely unfamiliar with the packages you are using, and know nothing about what is on your hard drive. For future reference: A) Read the Posting Guide. This is a plain text email list, and your html formatting gets removed leaving a mess that is not always readable. B) Most frequent users of R

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.

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPlot() is now available.

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPlot() is now available.

Hi all, I have a sequence file (fasta format) and want to calculate the rho statistics for dinucleotide abundance value on my data.. the code which I use is (using seqinr library and current working directory) seq_info<-read.fasta("gene.txt") rho(seq_info[1],2) but it yields only the dinucleotides, not their rho values, i.e, > rho(seq_info[1],2) aa ac ag at ca cc cg ct ga gc

Hi! I am trying to analyse my data using amova (http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova): My input to R is a DNA sequence file, format=fasta dna<- read.dna("XX.fasta", format="fasta") #left other options as default d<- dist.dna(dna, model="raw") g<- read.table("XXX.design") Load necessary libraries: library(pegas)

Hi - When I'm trying to read in a text file into a labeled character array, the memory stamp/footprint of R will exceed 4 gigs or more. I've seen this behavior on Mac OS X, Linux for AMD_64 and X86_64., and the R versions are 2.4, 2.4 and 2.2, respectively. So, it would seem that this is platform and R version independant. The file that I'm reading contains the upstream regions

When I try to load the DCluster package I get the following error message (R 2.5.1; PowerBook G4; Mac OS X 10.4.10) (Load needed package) Lade nötiges Paket: spdep (error: package spdep could not been loaded) Fehler: Paket 'spdep' konnte nicht geladen werden (additional warning message) Zusätzlich: Warning message: (There is no package spdep in:.....) es gibt kein Paket 'spdep'

Dear R users, I am glad to announce the release of a new package for R: DCluster. It implements a number of methods for the detection of clusters of disease. It includes methods to test Poisson extra-variation (Chi-square test and Potthoff-Whittinghill's test), Spatial Autocorrelation (Moran's I and Geary's c), general clustering (Whittermore's statistic and Tango's

Dear R users, I am glad to announce the release of a new package for R: DCluster. It implements a number of methods for the detection of clusters of disease. It includes methods to test Poisson extra-variation (Chi-square test and Potthoff-Whittinghill's test), Spatial Autocorrelation (Moran's I and Geary's c), general clustering (Whittermore's statistic and Tango's

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A

Hi I would like to use 'write.fasta(sequences, names, nbchar = 60, file.out, open = "w")' to convert a DNA sequence in a text file to fasta format. How do I read the the text file to prepare the argument 'sequences' of the function. The DNA sequence in the text file is one line as below: ATCACACAACGACACTCACCCTGGACGCTCATC......... Thank you [[alternative HTML

Hi everybody, I have a large fasta file(15M) which contains a lot of DNA sequence in fasta format.And i want to get probabilities matrix for 2nd order markov china from this background.Here is a web tool, http://tandem.bu.edu/markov.html.But i can not upload a large file. I wonder if there is a R packages can do this ,Thanks in advance . Jiantao Shi **

I am trying to pull a subset form a large group of FASTA sequences. I need to pull them based on the annot and write.fasta them. I have my subset annot titles in a .csv. What is the way to go about this? I tried pulling the sequences from a .csv but then MEGA 5 was not happy when i tried to put them back and I need to use MEGA to keep my data uniform. Any help would be greatly appreciated Thank