search for: readfasta

Hello dear R help group, I would like to download the tRNA data on: http://gtrnadb.ucsc.edu/download.html And then import it into R. Can anyone direct me as to how to do so? Thanks, Tal ---------------------------------------------- My contact information: Tal Galili E-mail: Tal.Galili@gmail.com Phone number: 972-52-7275845 FaceBook: Tal Galili My Blogs: http://www.talgalili.com (Web and

...presumably generates the right input data format. It would b very useful to get some example of CharacterToFASTArecords(x) usage. The on-line documentation reads: "For CharacterToFASTArecords, the (possibly named) character vector to be converted to a list of FASTA records as one returned by readFASTA" Since I have description and sequnce in separate variables ... I do not know how to use it. zz <- file (filname,"w") write(miRNA.rec, zz, append = FALSE) write(miRNA.seq,zz, append = TRUE) # geneDesc <- paste (">",gene.id, &quo...

...ight help me with the import/alignment. So far, I found two nice repositories that holds such data: 1) <http://trnadb.bioinf.uni-leipzig.de/Result> http://trnadb.bioinf.uni-leipzig.de/Result 2) <http://gtrnadb.ucsc.edu/download.html> http://gtrnadb.ucsc.edu/download.html And also the readFASTA command from Biostrings, that does basic importing of the data into R. My problem still remains with *how to handle the alignment* of the tRNA. Since I am not from the field, I might be missing a very basic answer (like where I should download the data from, what command to use or even where to a...

Hi, I want to group a large list (20 million) of strings into categories based on string similarity? The specific problem is: given a list of DNA sequence as below ACTCCCGCCGTTCGCGCGCAGCATGATCCTG ACTCCCGCCGTTCGCGCGCNNNNNNNNNNNN CAGGATCATGCTGCGCGCGAACGGCGGGAGT CAGGATCATGCTGCGCGCGAANNNNNNNNNN CAGGATCATGCTGCGCGCGNNNNNNNNNNNN ...... ..... NNNNNNNCCGTTCGCGCGCAGCATGATCCTG

...d 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 attempts. There is a new argument strip.desc to remove the leading '>' character in annotations (as in function readFASTA from the Biostrings package). The FASTA file example someORF.fsa from Biostrings is also added for comparisons. o Function read.alignment() has gained a new argument forceToLower defaulting to TRUE to force lower case in the character of the sequence (this is for a smoother interaction...

...d 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 attempts. There is a new argument strip.desc to remove the leading '>' character in annotations (as in function readFASTA from the Biostrings package). The FASTA file example someORF.fsa from Biostrings is also added for comparisons. o Function read.alignment() has gained a new argument forceToLower defaulting to TRUE to force lower case in the character of the sequence (this is for a smoother interaction...