search for: fasta

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. Here is my code: ####Get gene sequence from GenBank and store it as fasta...

...se excuse my brevity. On June 17, 2017 7:26:42 AM PDT, Mogjib Salek <mogjibs at gmail.com> wrote: >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. > >Here is my code: > >####Get gene seq...

...nux) system. We're transferring from one directory tree to another with a script that looks like: for i in /data2/* /data3/* do /usr/local/bin/rsync -a --delete ${i}/ /data1/`basename $i` done For some files/dirs, rsync is failing: rsync: rename "/data1/bordner/Pfam/version_22.0/fasta/.PF09720.fa.8z0Imb" -> "Pfam/version_22.0/fasta/PF09720.fa": File too large (27) rsync: rename "/data1/bordner/Pfam/version_22.0/fasta/.PF09721.fa.0OoTTG" -> "Pfam/version_22.0/fasta/PF09721.fa": File too large (27) rsync: rename "/data1/bordner/Pfam/ve...

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,...

...havior 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 of the yeast genome, with each upstream region labeled using a FASTA header, i.e.: FASTA header for gene 1 upstream region..... ..... .... FASTA header for gene 2 upstream.... .... The script I use - code below - opens the file, parses for a FASTA header, and then parses the header for the gene name. Once this is done, it reads the f...

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...

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: ATCACACAACGACACTCACCCTGG...

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. A...

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) Loading required package: adegenet Loading required package...

...or uco() when computing RSCU on sequences where an amino-acid is missing. There is now a new argument NA.rscu that allows the user to force the missing values to his favorite magic value. http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/uco.html o There was a bug in read.fasta(): some sequence names were truncated, this is now fixed (thanks to Marcus G. Daniels for pointing this). In order to be more consistent with standard functions such as read.table() or scan(), the file argument starts now with a lower case letter (i.e."file") in function re...

...or uco() when computing RSCU on sequences where an amino-acid is missing. There is now a new argument NA.rscu that allows the user to force the missing values to his favorite magic value. http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/uco.html o There was a bug in read.fasta(): some sequence names were truncated, this is now fixed (thanks to Marcus G. Daniels for pointing this). In order to be more consistent with standard functions such as read.table() or scan(), the file argument starts now with a lower case letter (i.e."file") in function re...

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] samp=paste("ANG_AUT.N.",list[i,8],"-1_1sA_&...

...o","k=btg@") # do a query ( it means : give me the sequences associated to the keywords begining with btg, save the list in toto) > socket <- banknameSocket$socket # here I save the socket in "socket" > request="extractseqs&lrank=2&format=\"fasta\"&operation=\"simple\"&zlib=F" # writing a request > #( it means : give me the sequence information of the list of rank 2 ( toto) in fasta format, no compressed > writeLines(request, socket, sep = "\n") # put the request into the socket > seq &l...

Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape package to read this file, then I convert this file into a genind object with DNA2genind function provide in adegenet package). After convert my file the pairwise.fst function is not found. If you could help...

...or instance with a sequence like NNNNNNNNNNNN). The argument oldGC is now deprecated and a warning is issued. Functions GC1(), GC2(), GC3() are now simple wrappers for the more general GCpos() function. The new argument frame allows to take the frame into account for CDS. o Function read.fasta() now supports comment lines starting by a semicolon character in FASTA files. An example of such a file is provided in sequences/legacy.fasta. The argument File is now deprecated. There is a new argument seqonly to import just the sequences without names, annotations and coercion attempt...

...or instance with a sequence like NNNNNNNNNNNN). The argument oldGC is now deprecated and a warning is issued. Functions GC1(), GC2(), GC3() are now simple wrappers for the more general GCpos() function. The new argument frame allows to take the frame into account for CDS. o Function read.fasta() now supports comment lines starting by a semicolon character in FASTA files. An example of such a file is provided in sequences/legacy.fasta. The argument File is now deprecated. There is a new argument seqonly to import just the sequences without names, annotations and coercion attempt...

I tried the following, obviously it didn't work. Hope you get my point, how to do it in R ? My objective is to read a large fasta file (but not storing the entire data into memory) , and compute some sequence composition statistics. while(a <- readLines("test1") != EOF) print(a) _________________________________________________________________ [[alternative HTML version deleted]]

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 t...

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..

Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following: > nml [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b" [3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7c"...