where to get library RbcBook1
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Xueli Liu ▴ 10
@xueli-liu-1358
Last seen 9.6 years ago
Dear all, I am wondering where to download the library RbcBook1. I download bionconductor successfully and when I use some sample code for clustering to load the library of RbcBook1, it gives the following error message: Error in open.connection(con, "rb") : unable to open connection In addition: Warning message: cannot open compressed file 'C:/PROGRA~1/R/rw2011/library/RbcBook1/R/all.rda' Error in library(RbcBook1) : .First.lib failed for 'RbcBook1' Thanks a lot for your help! Xueli
RbcBook1 RbcBook1 • 1.1k views
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Paul Grosu ▴ 10
@paul-grosu-1359
Last seen 9.6 years ago
Hi - Anyone know how I can get the nucleotide sequence(s) to a GeneID? Here is an example: Let's say I have the following gene ID (960) and below is the link to it on NCBI: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dop t=Graphics&list_uids=960#ubor85_RefSeq when I do the following commands: library(annotate) getSEQ("960") I get: [1] "LLGKILVITLVQNFGREFTLEFLAAYPKVVAGVANALAYKYHWDPSLFL" But these gene has several variants so I wanted to find the different sequence variants which I'm having trouble figuring out from the AnnBuilder or annotate packages. Thanks, Paul
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On Jul 25, 2005, at 3:46 PM, Paul Grosu wrote: > > Hi - > > Anyone know how I can get the nucleotide sequence(s) to a GeneID? > > Here is an example: > > Let's say I have the following gene ID (960) and below is the link to > it on NCBI: > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? > db=gene&cmd=Retrieve&dopt=Graphics&list_uids=960#ubor85_RefSeq > > when I do the following commands: > > library(annotate) > getSEQ("960") If you look at the help for getSEQ, it takes a GenBank accession number, not a GeneID, as an argument (and the two are quite different). > But these gene has several variants so I wanted to find the different > sequence variants which I'm having trouble figuring out from the > AnnBuilder or annotate packages. > If you want the sequences for a given GeneID, you are probably talking about RefSeq sequences. There may be an easier way using one of the annotation packages, but this is pretty easy, also. Grab the refseq to GeneID mapping file from the web at: ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz gunzip the file and then load it into R (which will take a few minutes--big file): gene2refseq <- read.table('gene2refseq',sep="\t",header=FALSE) The documentation for the columns is included below. The second column of the resulting data frame contains GeneID. The fifth column contains the GI number for the nucleotide sequence. Therefore, you can do something like: generows <- which(gene2refseq[,2]==960) sequences <- sapply(gene2refseq[generows,4],getSEQ) Sequences now has 5 sequences, corresponding to the 5 RefSeq sequences associated with your gene. You hopefully get the idea. As for your gene having multiple isoforms, there are 5 RefSeqs for GeneID 960, so you will end up with 5 sequences. I would also look at UCSC or EnsEMBL, both of which can find your sequences based on GeneID via the web in batch mode. I have only shown one way in R to do it. Hope this helps, Sean DOCUMENTATION from NCBI for gene2refseq file ====================================================================== == === gene2refseq ---------------------------------------------------------------------- -- --- This file can be considered as the logical equivalent of ftp://ftp.ncbi.nih.gov/refseq/LocusLink/loc2ref tab-delimited one line per genomic/RNA/protein set of RefSeqs ---------------------------------------------------------------------- -- --- tax_id: the unique identifier provided by NCBI Taxonomy for the species or strain/isolate GeneID: the unique identifier for a gene --note: for genomes previously available from LocusLink, the identifiers are equivalent status: status of the RefSeq RNA nucleotide accession.version may be null (-) for some genomes RNA nucleotide gi the gi for an RNA nucleotide accession, '-' if not applicable protein accession.version will be null (-) for RNA-coding genes protein gi: the gi for a protein accession, '-' if not applicable genomic nucleotide accession.version may be null (-) if a RefSeq was provided after the genomic accession was submitted genomic nucleotide gi the gi for a genomic nucleotide accession, '-' if not applicable start position on the genomic accession position of the gene feature on the genomic accession, '-' if not applicable position 0-based end positon on the genomic accession position of the gene feature on the genomic accession, '-' if not applicable position 0-based orientation orientation of the gene feature on the genomic accession, '?' if not applicable
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