Do you know any other place than UniProt to get this kind of data. I would like to get a file with all sequences without much hassle.
I used http://www.uniprot.org/uniprot/?query=organism%3A%22Helicobacter+pylori+26695%22&sort=score query and I got 2 proteins :|
I would get such data from NCBI RefSeq. The directory for Helicobacter pylori 26695 is:
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Helicobacter_pylori_26695_uid57787/
There you can find sequences in a variety of formats. What you need is probably NC_000915.faa, which is a FASTA file with all the translation products (proteins).
It's great! It is exactly what I wanted.
I got the same number of protein (at least close) when I used http://www.uniprot.org/taxonomy/?query=strain%3A26695&sort=score
What do you think? Is it significant different. I had already proteins from UniProt in my local database. Should I stick to them or should I download data from NCBI RefSeq?
http://www.uniprot.org/uniprot/?query=organism:210+keyword:181 would give the heliobacter_pylori complete proteome as defined by uniprot. However, I am not sure which strain that would be. Will ask around
Which database to use is largely a subjective choice. It is difficult to know up front if the proteome provided by UniProt is better or worse than that provided by RefSeq. The main advantage that I see of using RefSeq is that it is based on a specific fully sequenced genome, for which reason I can be sure that it is a complete proteome. UniProt - not being a genome database - might in some cases give you a very partial proteome. But I guess you will have to judge on a case-by-case basis.
Do you have to use UNIPROT?
I searched for your strain in NCBI's taxonomy database and got this page.
On the right there are several links for Nucleotide, Protein, Genomes, etc... Click "Protein" and arrive here
If you want to download the sequences, click 'send to'.
what about integr8 at the ebi? http://www.ebi.ac.uk/integr8/FtpSearch.do?orgProteomeId=23 all the proteome set is available.
I'd do this. using the advanced search
Here you can find more info about what "Complete proteome" keyword means
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version 2.3.6
helicobacter AND pylori AND strain:26695 gives better result. However I'm still not quite sure if the procedure is correct.
maybe you could try taxonomy:"Helicobacter pylori" so you could get all the proteins for all the H. pylori when was the H. pylori 26695 genome sequenced? If it's too recent maybe proteins are not in the Uniprot db yet