How can I download C. briggsae 3 UTRs in bulk?
We don’t really have a strictly empirical set of 3′ UTRs (3′ flanking sequences taking from cDNA). However, what you probably really want are predicted 3′ UTR regions. Those, you can get by going to the Genome Dumper: http://wormbase.org/db/searches/advanced/dumper selecting the species “C. briggsae”, and then filling in the options for the download that you want. The main stumbling block is that the list you need for briggsae genomic sequences is rather long. However, I’ve tried typing this: cb25.* into the window “Type in a list of sequence or chromosome names”, and that seems to successfully prompt the Genome Dumper to search through all available C. briggsae genomic contigs. Also, you should pick the “Integrated (‘hybrid’) briggsae gene set”, and select some reasonable value (e.g., 1000 bp) for the length of the 3′ flank sequences that you want.
