[Feedback] Site Feedback: Fetch Genomic Alignments from Gramene

[Marcela K. Monaco]

Hi Tom,

You may get the multiple alignments used to build our gene trees (EMF) from:
ftp://ftp.ensemblgenomes.org/pub/plants/release-22/emf/ensembl-compara/

This is a link in the "Comparative genomics" section of every species page
in Gramene and Ensembl Plants, but is currently misspelled on our end
(sorry, it will be fixed shortly).

Marcela


On Thu, May 15, 2014 at 12:19 PM, feedback at gramene.org <feedback at gramene.org
> wrote:

> URL         : http://www.gramene.org/web-services
>
> Subject     : Site Feedback: Fetch Genomic Alignments from Gramene
>
> Name        : Tom Kono
>
> Email       : konox006 at umn.edu
>
> Organization: University of Minnesota
>
> Comments    :
>
> Hello,
>
> We am interested in downloading the DNA-DNA genomic alignments between
> barley and related species (T. urartu, A. tauschii, B. distachyon, and O.
> sativa). We notice that through the web interface, we can only fetch a
> maximum of 5Mb.
>
> We have looked at the various ways to programmatically fetch data, and
> tried to connect to the MySQL database. However, we are unable to find a
> way to download the complete genomic alignments between these species. Is
> there a way we could get access through this data, either through a SQL
> database, or an FTP server? Thank you very much.
>
> http://www.warelab.org/bugs/view.php?id=4941
>
>
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>
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