[BioC] reverse complement or no reverse complemnt on biomaRt / biomart.org
James W. MacDonald
jmacdon at med.umich.edu
Tue Oct 13 16:21:46 CEST 2009
Hi Tefina,
Tefina Paloma wrote:
> Dear Jim,
>
> Do you know if these sequences are sense or antisense?
> If you export the sequence via biomart (via the webpage), you get the following:
>
>> ENST00000280193 utr5:KNOWN_protein_coding
> CGGGGAAGGGGAGGGAGGAGGGGGACGAGGGCTCTGGCGGGTTTGGAGGGGCTGAACATC
> GCGGGGTGTTCTGGTGTCCCCCGCCCCGCCTCTCCAAAAAGCTACACCGACGCGGACCGC
> GGCGGCGTCCTCCCTCGCCCTCGCTTCACCTCGCGGGCTCCGAATGCGGGGAGCTCGGAT
> GTCCGGTTTCCTGTGAGGCTTTTACCTGACACCCGCCGCCTTTCCCCGGCACTGGCTGGG
> AGGGCGCCCTGCAAAGTTGGGAACGCGGAGCCCCGGACCCGCTCCCGCCGCCTCCGGCTC
> GCCCAGGGGGGGTCGCCGGGAGGAGCCCGGGGGAGAGGGACCAGGAGGGGCCCGCGGCCT
> CGCAGGGGCGCCCGCGCCCCCACCCCTGCCCCCGCCAGCGGACCGGTCCCCCACCCCCGG
> TCCTTCCACC
>
>> 5' Flanking sequence chromosome:GRCh37:4:177713896:177713945:1
> AAGTGAGAGGAGCCGGGCCGCGGGCGCTGCGGCGGGGGCGCTGGCGGCGG
How are you getting this? I get the same thing as the web service, as I
noted yesterday:
> getSequence(id = c("ENST00000280193"), type
="ensembl_transcript_id",seqType = "transcript_flank", upstream = 50,
mart =mart)
transcript_flank ensembl_transcript_id
1 CCGCCGCCAGCGCCCCCGCCGCAGCGCCCGCGGCCCGGCTCCTCTCACTT ENST00000280193
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-21 r49780)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] biomaRt_2.1.0 annaffy_1.17.2 affycoretools_1.17.4
[4] KEGG.db_2.3.0 GO.db_2.3.0 RSQLite_0.7-2
[7] DBI_0.2-4 AnnotationDbi_1.7.17 affy_1.23.9
[10] Biobase_2.5.6
loaded via a namespace (and not attached):
[1] affyio_1.13.5 annotate_1.23.2 Biostrings_2.13.50
[4] Category_2.11.4 gcrma_2.17.2 genefilter_1.25.7
[7] GOstats_2.11.3 graph_1.23.6 GSEABase_1.7.3
[10] IRanges_1.3.89 limma_2.19.4 preprocessCore_1.7.9
[13] RBGL_1.21.12 RCurl_0.98-1 splines_2.10.0
[16] survival_2.35-7 tools_2.10.0 XML_2.5-1
[19] xtable_1.5-5
Best,
Jim
>
> So, in contrast to the web-view, the flanking sequence is reverse complemented.
> Basically it is just a problem of correct definition and assignment.
> So which sequences are sense and which are antisense.
>
> Best,
> Tefina
>
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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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