search for: genbank

Hi, I am trying to work with the ape package, and there is one thing I am struggling with. When calling the *read.GenBank()* function, I can get it to work with an object created like this: *>x <- c("AY395554","AY611035", ...)* *>read.GenBank(x)* However, I am trying to use the function to fetch several hundred sequences at once. So I have been testing with small files, but cannot get t...

So basically I have made a HTML file with a table in it. Column 3 contains a GenBank number and is always proceeded by "=GenBank">". I want to read the file and return the number which comes directly after this (the contents of column 3). Ideally I would like to save this number as a string for use later in the script, but any help is good help. Been at this fo...

Hi I am trying to read genbank est flat files. Is there any function in R to do that. I was looking for something similar to SeqIO.parse(input_handle, "genbank") in bioPython that convert the genebank sequence into fasta sequence. (One option is to call biopython from R but I am not familiar with python functions so I...

...low) 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. Here is my code: ####Get gene sequence from GenBank and store it as fasta file ####16 June 2017 #1- Set the working directory and make sure the right libraries are installed (make sure 'ape' and 'seqinr' packages are installed) WD <- "~Documents/Scripting/R_Studio/Sequences/" setwd <- (WD) #2- Fetch a sequence ( be...

I just ran this again and got this error: leelab/NCBI_Data_old/GenBank/htg write failed on leelab/NCBI_Data_old/GenBank/htg : Error 0 rsync error: error in file IO (code 11) at receiver.c(243) Received signal 16. (no core) rsync error: received SIGUSR1 or SIGINT (code 20) at rsync.c(229) The command I am running is: /usr/local/bin/rsync -auv --delete --rsh=/usr/bin...

...>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. > >Here is my code: > >####Get gene sequence from GenBank and store it as fasta file >####16 June 2017 > >#1- Set the working directory and make sure the right libraries are >installed >(make sure 'ape' and 'seqinr' packages are installed) > >WD <- "~Documents/Scripting/R_Studio/Sequences/" >setwd <-...

I'm trying to rsync a filesystem from a Solaris 7 server to a Solaris 8 server. I keep getting the following message when rsync attempts to update a particular file: write failed on leelab/NCBI_Data/GenBank/htg : Error 0 rsync error: error in file IO (code 11) at receiver.c(243) Received signal 16. (no core) rsync: connection unexpectedly closed (22672537 bytes read so far) rsync error: error in rsync protocol data stream (code 12) at io.c(140) The file it is getting the error on is very large: -rw...

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

Anyone have any experience with MpiBlast and Lustre. We have MpiBlast-1.4.0-pio and lustre-1.6.3 and we are seeing some pretty poor performance with most of the mpiblast threads spending 20% to 50% of their time in disk wait. We have the genbank nt database split into 24 fragments (one for each of our OSTs, 3 per OSS). The individual fragments are not striped due to the ldlm_poold issue so that should not be the problem. Should we not be using the PIO (ROM-IO) version of MPIBlast w/ lustre? I''m wondering if there are so...

...ing 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. Emmanuel Paradis Laboratoire de Pal?ontologie Institut d...

Hello! I don't know if there is some R-package able to associate ontology to a long list of GeneBank Name (a txt-tab file or an XML file), i.e. I would as output a formatted file with 4 columns (1:GeneBank Name 2,3,4:ontology). I know that I have to perform a mapping of genes, I got a look on AnnBuilder pkg, but I 've not idea from where to start. Some suggestion? Thanks in advance!

CRAN (and crantastic) updates this week New packages ------------ * Bergm (1.0) Alberto Caimo http://crantastic.org/packages/Bergm Functions implementing Bayesian estimation for exponential random graph models via exchange algorithm Updated packages ---------------- lmtest (0.9-26), logcondens (1.3.5), MTSKNN (0.0-4), pmml (1.2.21), r2lUniv (0.9.4), rattle (2.5.11), rgdal (0.6-23),

...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 function extracts the coding sequence annotations from a GenBank format file. This function is specifically designed for eukaryotic sequences, i.e. with introns. The output file will contain the coordinates of the exons, along with the name of the CDS to which they belong. o After an e-mail by Marcelo Bertalan on 26 Mar 2007, a bug in oriloc() when th...

...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 function extracts the coding sequence annotations from a GenBank format file. This function is specifically designed for eukaryotic sequences, i.e. with introns. The output file will contain the coordinates of the exons, along with the name of the CDS to which they belong. o After an e-mail by Marcelo Bertalan on 26 Mar 2007, a bug in oriloc() when th...

...diction, e.g., linear models, machine learning, and other multivariate analysis methods. * Programming experience and ability to write R and Perl script. * The candidate will have experience with large-scale genomics data and a solid understanding of bioinformatics data bases (eg: GenBank, RefSeq, dbSNP etc) * Experience with some bioinformatics software such as: Spotfire, Partek, Ingenuity, GeneGo, Balst, and Blat. * The candidate will have the ability and interest in learning new techniques and skills in accordance with evolving research program needs. *...

...f" > pgfFile <- "RaGene-1_0-st-v1.r4.pgf/RaGene-1_0-st-v1.r4.pgf" > pkg <- new("AffyGenePDInfoPkgSeed", author="Anne-Marie Madore", email="anne-marie.madore.1@ulaval.ca", version="0.0.1", + genomebuild="RefSeq April 3, 2007, GenBank® January 25, 2007, Rat Ensembl transcripts April 3, 2007 ", + biocViews="AnnotationData", pgfFile=pgfFile, clfFile=clfFile, transFile=transFile, probeFile=probeFile) > makePdInfoPackage(pkg, destDir=".") Creating package in ./pd.ragene.1.0.st.v1 loadUnitsByBatch too...