I read that message and asked for some guidelines to query  biomaRt in batch mode.
The PDF file available from biomaRt on-line pages shows a number of useful ways to extract useful data but it 
does not mention any batch interrogation mode.
I thought R CMD BATCH would be the way to do that. If so it will take a while.

Basically I am trying to extract the 3utr sequence for each target gene transcript listed in data set hsTargets.
Since I have to save to a file the miRNA identifier, the miRNA sequence, followed by all its target  gene transcripts with their 3utr sequences, my R script  loops on each miRNA identifier, reads out all its target gene transcript identifiers  from 
hsTargets, and subits such an ENST  list to biomaRt  to get the relative 3UTR sequences:

## -------------------- GET 3UTR SEQUENCES FOR TARGET GENE TRANSCRIPTS
    gene_seq <- getSequence (id=tmp[,"target"],type="ensembl_transcript_id",seqType="3utr",mart=hmart) 

In addition, to the purpose of identifying the target transcripts in the output file I also ask biomaRt for some other target identifiers providing the ENST filter:

 gene_map <- getBM(attributes=c("hgnc_symbol","ensembl_gene_id","refseq_dna","ensembl_transcript_id"),
                                        filters = "ensembl_transcript_id", values=gene_seq[j,"ensembl_transcript_id"], mart=hmart)

The  typical output file looks like the  example pasted at the bottom.
My question is: how can I rewrite my R script so as to accomplish my task in batch mode ?
I hope I won't have to get all the 3utr sequences  for all the target gene transcripts listed in hsTargets. together.

Thank you,
Maura

>hsa-miR-7
UGGAAGACUAGUGAUUUUGUUGU   UGGAAGACUAGUGAUUUUGUUGU
>GPRC5A|ENSG00000013588|ENST00000014914
CTCTGTCCTGAA ............................................................................................................................................................................
.............................................................................................................................................................................................................
>PSMA4|ENSG00000041357|ENST00000044462
AATCAGAGATTTTATTACTCATTTGGGGCACCATTTCAGTGTAAAAGCAGTCCTACTCTTCCACACTAGGAAGGCTTTAC
TTTTTTTAACTGGTGCAGTGGGAAAATA.......................................................................................................................................
.............................................................................................................................................................................................................
>COPZ2|ENSG00000005243|ENST00000006101
AGGCTGTGGATTCAAGGCTCCCTGCCCCCCAGATCATTTCCCCAA...................................................................................
.............................................................................................................................................................................................................
>PIGB|ENSG00000069943|ENST00000164305
ACTTTCCTAGATAAATTAACATT....................................................................................................................................................
.............................................................................................................................................................................................................
>ZNF275|ENSG00000063587|ENST00000095634
AAACGCCCTGTGGTCCCGCGGGACAGGGACGGAGTCCCCAGAGGGGATGGCAGAGTCAAAGGAGATGAACAGTTTT
GTAGCGCTTATATATTTTGT..........................................................................................................................................................
............................................................................................................................................................................................................












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