I am trying to download gene sequences of all Ensembl organisms in fasta format including:
Vertebrates, Metazoa, Plants, Fungi, Bacteria and Protists
In the past I worked only with vertebrates, therefore I downloaded the whole genome and the matching gff file via ensembl ftp site.
Thereafter I extracted the protein-coding gene sequences using bedtools getfasta command.
Now I want to do the same process for all the organisms and not only vertebrates, but the problem is that I limited with memory.
Is there any way to download the gene sequences directly with no need to download the whole genome file?
It wouldn't help me to download the cDNA sequences sine I am interested also in the introns.