How can I download C. elegans-C.briggsae orthologs and their protein-coding DNA sequences?
One possible way to retrieve those would be to download a C. elegans-C.briggsae ortholog file: ftp://ftp.wormbase.org/pub/wormbase/briggsae/supporting_data_stein_2003/orthologs_and_orphans/orthologs.txt and C. briggsae gene sequences in fasta format (briggenes.fa.gz): ftp://ftp.wormbase.org/pub/wormbase/briggsae/ and write a script that would parse C. briggsae ortholog sequences based on C. elegans gene names. Another way would be to use WormMart to get a list of genes with orthologs (filter by Homolog/Ortholog -> Homolog[Compara Orholog]). in the Attribute part you can select if you want to have the sequences or just a table of orthologs.
