Dear all,

I used to use MySQL mode of biomaRt to retrieve genomic sequence using simple chromosome coordinate (e.g. chr 1, 100000-100100). I did work fine. However, recently I update biomaRt to 2.6.0, and found that MySQL mode was no longer implemented, at least in the same way. Could anybody tell me how to use MySQL mode with biomaRt 2.6.0, or if there is alternative way to get genomic sequence using simple chromosome coordinate?

Below is  the error message I got;

> library("biomaRt")
> ensembl = useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl", mysql=TRUE)
Error in useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl",  : 
  unused argument(s) (mysql = TRUE)
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.6.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-3 XML_3.2-0  

Thank you!
Takashi
------------------------------------------------------------
The Salk Institute for Biological Studies
10010 North Torrey Pines Rd., La Jolla, CA 92037
Phone: +1-858-453-4100 x1788
FAX: +1-858-455-7933
Email: takashi@salk.edu

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