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Scott Ochsner
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300
@scott-ochsner-599
Last seen 10.3 years ago
Dear list,
I am trying to retrieve zfin annotation for each of my 6000+ zebrafish
EST ids using biomaRt. As an example of the EST ids I've included the
output from NCBI's EST search for CO349769.
1. DR_AOV_FL01_G08 adult ovary full-length (TLL) Danio rerio cDNA,
mRNA sequence
gi|49431086|gb|CO349769.1|[49431086]
As a further note, searching UniGene is successful with "CO349769",
but not with "49431086". I've set up the following:
>library(biomaRt)
>ensembl=useMart("ensembl",dataset="drerio_gene_ensembl"))
Question1: If ESTs are mapped (based on previous posts they don't
look like they are), what is the appropriate filter variable in the
line of code below?
>map<-getBM(attributes=c("zfin_id","zfin_symbol"),filters="?",values="
CO349769",mart=ensembl)
Question2: If it turns out ESTs are not mapped, I'll probably have to
go through UniGene to obtain an ID I can use with biomaRt. Does
anyone know of a way to batch search UniGene? 6000+ ids is a lot to
search one by one.
Thanks for any help,
> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] splines tools stats graphics grDevices utils
datasets methods base
other attached packages:
[1] biomaRt_1.16.0 genefilter_1.22.0 survival_2.34-1
geneplotter_1.20.0 annotate_1.20.0 xtable_1.5-4
AnnotationDbi_1.4.0 lattice_0.17-15
[9] limma_2.16.2 affy_1.20.0 Biobase_2.2.0
loaded via a namespace (and not attached):
[1] affyio_1.10.0 DBI_0.2-4 grid_2.8.0
KernSmooth_2.22-22 preprocessCore_1.4.0 RColorBrewer_1.0-2
RCurl_0.91-0
[8] RSQLite_0.7-1 XML_1.94-0.1
Scott A. Ochsner, Ph.D.
NURSA Bioinformatics
Molecular and Cellular Biology
Baylor College of Medicine
Houston, TX. 77030
phone: 713-798-6227