similar to: FASTA annot issue

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 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 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 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

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 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 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

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

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

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

I am trying to return an index for a data set by searching using filenames. The name may be ANG_AUT.N.0734C70411A-1_1sA_0734C70411A.fasta, but i'd just like to search it using the term "0734C70411" as the file may be 0734C70411A or 0734C70411C or 0734C70411D Any way to do this other than doing something like this. where 0734C70411A is part of matrix list[,8]

Hello, I have a problem, when I run read.fasta.pdb I get this error: pdb/seq: 1 name: dcluster.1 Error: subscript out of bounds My FASTA file is the sequence of the bovine insuline. Thanks in advance, Rg -- View this message in context: http://n4.nabble.com/problem-with-bio3d-package-tp1012116p1012116.html Sent from the R help mailing list archive at Nabble.com.

I realize function write FASTA expects a list with two items, respectively, description and sequence. However, just passing a list won't work (please, see code at the bottom of this message) I saw there is the helper function CharacterToFASTArecords(x) that presumably generates the right input data format. It would b very useful to get some example of CharacterToFASTArecords(x) usage. The

Dear all, I have DNA sequence data which are fasta-formatted as >gene A;..... AAAAACCCC TTTTTGGGG CCCTTTTTT >gene B;.... CCCCCAAAA GGGGGTTTT I want to load only the lines that start with ">" where the annotation information for the gene is contained. In principle, I can remove the sequences before loading or after loading all the lines. I just wonder if there's a way to

Dear useR's I have a small basic problem which I am hoping to get some help with. I have a data frame, testSeq_df, with 1 row and 500 columns. Each column is a character (a,c,g or t). I want this sequence to have 4 factors (a,c,g,t). When I try the following: for(i in 1:500){ if (length(levels(testSeq_df[,i]))==1) levels(testSeq_df[,i]) <-

https://bugs.freedesktop.org/show_bug.cgi?id=58378 --- Comment #22 from Andreas Loew <awl1 at gmx.net> --- Hello Ilia, regarding (a) and (b): I am just waiting for a rpmbuild of an OL6 version of 3.13-rc3 to finish and will report back on my findings and include a dmesg output from that version. Regarding (c): Would'nt it make more sense than starting with 3.6 release and 3.7 release

 Sir,  I am a student in biostat and bioinformatics.  I am interested to use R for my research work related to codon usage analysis.This software was used in a publication entitled " Online synonymous codon usage analyses with the ade4 and seqinR packages" and a weblink  http://pbil.univ-lyon1.fr/datasets/charif04/ was given for readers to use the program. Now  I would like to use the