[BioC] Help with getBM using EST ids from zebrafish

Ochsner, Scott A sochsner at bcm.tmc.edu
Thu Dec 4 21:14:13 CET 2008

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

As a further note, searching UniGene is successful with "CO349769", but not with "49431086".  I've set up the following:


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?


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) 

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 

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