FTP sites down, WormMart down, where do I find gff3 files?

Model Organism: Worms WormBase
1

I’m getting timeouts on both
http://caprica.caltech.edu:9002/biomart/martview/

and

ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF3

I’d like to simply download gff3 files that tell me where the coding regions, exons, etc are for a given genome build. Does anyone have any mirrors for this data?

2

WormMart has been retired:

WormMart Sunset Period: to be retired 01 Jan 2016
November 13, 2015 by Todd Harris Leave a Comment

Today we are announcing the “sunset” period for WormMart at WormBase. WormMart will be formally retired from WormBase at the end of 2015.

For many years, WormMart was the primary data mining facility at WormBase. Later, we replaced it with WormMine based on the Intermine platform. In that time, we have maintained the two in parallel, although WormMart updates were frozen at the WS220 release of WormBase.

I don’t know if that “WormMine” link will help, but it’s worth a try.

3

From WormBase, select the pulldown Tools > More Tools > Downloads, log in as guest to the FTP site, then drill down to download the GFF of interest (releases > WS250 > species > c_elegans > PRJNA13758 > gff3.gz).

4

Prompted by Harold’s reply, I looked at ftp.wormbase.org, and think I know why you’re getting a timeout when you try the WormBase ftp site. The address you’re trying to use (ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF3) calls for a folder (ftp://ftp.wormbase.org/pub/wormbase/genomes) that appears not to exist.

5

Thanks! Sperm or Egg’s reply is on point.