I am trying to DNA sequence of the upstream regulatory region of a number of genes using the biomaRt package. I start with a list of EntrezGene IDs and would like to extract the sequence from 10Kb upstream of the end of the 5'UTR to the end of the 5'UTR. I wrote a neat little package of scripts to do this with biomaRt and export the data in .FASTA format. I have found that this works well when I search for one gene at a time. But when I input a list of entrez gene ids to the getSequence function it gives me back sequences but the sequences do not always match the answer I get when I search for the gene one at a time. Sending calls to biomaRt one gene at a time will clearly be much slower but fast searches do me little good if I don't know whether the answer is correct or not. The codes I have written are pretty straight forward. The meat of the code is the getSequence function which I call as follows: biomart<- useMart('ensembl') martDataset<-useDataset(dataset,mart=biomart) getSequence(id = '6720', type='entrezgene',seqType = 'coding_gene_flank',upstream = 10000, mart = martDataset) As an example, when I search the 5869 gene by itself, I get the same answer provided by the biomart web based tool. When I search for the 5869 gene in a list like the following list, I get a different sequence. c('8317','1435','1063','4751','3832','3070','5869','675','81624','7249 ','1186','3801','672','1058','22974','23654','4171','1062','3148','400 1','3007','26271','9314') Thanks for any help with this problem. This exact application is shown in the biomaRt vignette. Not sure where my application is going wrong. Let me know if you need more info. I am open to other ways of solving this problem without biomaRt getSequence. Thanks, Michael Gormley [[alternative HTML version deleted]]