[BioC] reverse complement or no reverse complemnt on biomaRt / biomart.org
James W. MacDonald
jmacdon at med.umich.edu
Mon Oct 12 17:57:07 CEST 2009
Tefina Paloma wrote:
> Dear list,
> having a look at the vegfc gene (located on the reverse strand) on the
> website of biomart and querying the 5utr and the flanking sequence yields
> the following:
> Doing the same in R, yields essentially the same with the only difference
> that in the case of the flanking sequence the reverse complement is given:
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> vegfc_fs = getSequence(id = c("ENST00000280193"), type =
> seqType = "transcript_flank", upstream = 3000,
> mart = ensembl)
> vegfc_utr = getSequence(id = c("ENST00000280193"), type =
> seqType = "5utr", mart = ensembl)
> As the gene is located on the reverse strand, one would probably be
> interested in the reverse complement of the sequence returned by
> Although it's nice that the flanking sequence is already reverse
> complemented in R, it should be somehow documented.
The flanking sequence isn't reverse complemented in R, it is reported
exactly as it is received from the Biomart server.
I am a bit confused here as well; AFAICT, the sequence for the 5' flank
and UTR are identical from all sources (Ensembl, Biomart and biomaRt).
> And the question arises, why does biomaRt only return the reverse complement
> of the flanking sequence but not of the utr?
> I would appreciate any hints!
> Thanks a lot in advance,
> R version 2.9.1 (2009-06-26)
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  Biostrings_2.12.8 IRanges_1.2.3 biomaRt_2.0.0
> loaded via a namespace (and not attached):
>  Biobase_2.4.1 RCurl_0.98-1 XML_2.5-3
> [[alternative HTML version deleted]]
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James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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