Dowloading All Protein Sequences

Question

[Pappu]

I downloaded the trembl database from uniprot website. But it does not seem to contaln all the protein sequences. I am wondering which database contains all entries (RefSeq?) and how to download a fasta of it.

Answer 1

[Chris Cole]

You need to clarify what you mean by 'all protein sequences'. Which ones are missing from trEMBL? In which species?

If you genuinely are after all RefSeq sequences then you're not going to find them in trEMBL. Try RefSeq at NCBI: http://www.ncbi.nlm.nih.gov/refseq/

Answer 2

[Biojl]

You can download the protein (or nucleotide) sequences in FASTA format for vertebrates and other eukaryotic species from Ensembl:

http://www.ensembl.org/info/data/ftp/index.html