Dear list,

About over a year ago, I extracted 3'UTR sequences for about 7000  
genes using Biomart for my project. This is the command that I used:

(my gene_list is in gene symbol)
 >my_mart = useMart("ensembl",dataset="hsapiens_gene_ensembl")
 >seq_3utr = getSequence(id = unique(gene.symbol),  
type="hgnc_symbol",seqType="3utr",mart = my_mart)
 >seq_3utr = seq_3utr[seq_3utr[,"3utr"] != "Sequence unavailable",]
 >here: extract longest 3'UTR for each unique gene symbol
 >exportFASTA(seq_3utr, file=paste("s3utr.fa",sep=""))

As my project goes, I now need 3'UTR genomic coordinates to get  
phastcons conservation for some regions in 3'UTR.
To do that, I first convert hgnc_symbol back to ensembl_gene_id, then  
get 3'UTR coordinates using getBM like this:

 >s3utr = read.DNAStringSet(paste("s3utr.fa",sep=""),format="fasta")
 >gene_names = names(s3utr)
 >hgnc2ensembl  = getBM(attributes=c("hgnc_symbol","ensembl_gene_id"),  
filters="hgnc_symbol", values=gene_names, mart=my_mart)
 >s3utr_pos  = getBM(attributes=c("ensembl_gene_id",  
"chromosome_name","strand","3_utr_start", "3_utr_end"),
		filters="ensembl_gene_id", values=as.character(hgnc2ensembl 
$ensembl_gene_id), mart=my_mart)
 >s3utr_pos = s3utr_pos[complete.cases(s3utr_pos),]

By doing that, now I can only get about 5000 gene symbols with 3'UTR  
coordinates (converting from hgnc_symbol back to ensembl_gene_id  
looses about 250 genes). I was thinking it might be version  
difference? So I tried to use ensembl archive but it gives me error as  
below:

 > my_mart =  
useMart("ensembl_mart_50",dataset="hsapiens_gene_ensembl",archive=T)
Error in value[[3L]](cond) :
   Request to BioMart web service failed. Verify if you are still  
connected to the internet.  Alternatively the BioMart web service is  
temporarily down.
In addition: Warning message:
In file(file, "r") : cannot open: HTTP status was '404 Not Found'

Is there anyway that I can get 3'UTR coordinates for all my gene list?

Thanks for any help.

Jean
	[[alternative HTML version deleted]]

