Question: How To Get A Full Proteome Of Helicobacter Pylori 26695.
2
gravatar for Marcinmagnus
8.9 years ago by
Marcinmagnus80
Marcinmagnus80 wrote:

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 :|

protein uniprot • 2.7k views
ADD COMMENTlink modified 8.9 years ago by Marina Manrique1.3k • written 8.9 years ago by Marcinmagnus80

helicobacter AND pylori AND strain:26695 gives better result. However I'm still not quite sure if the procedure is correct.

ADD REPLYlink modified 3 months ago by RamRS25k • written 8.9 years ago by Marcinmagnus80

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

ADD REPLYlink written 8.9 years ago by Marina Manrique1.3k
3
gravatar for Lars Juhl Jensen
8.9 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

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).

ADD COMMENTlink written 8.9 years ago by Lars Juhl Jensen11k

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?

ADD REPLYlink modified 3 months ago by RamRS25k • written 8.9 years ago by Marcinmagnus80

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

ADD REPLYlink modified 3 months ago by RamRS25k • written 8.9 years ago by Jerven640

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.

ADD REPLYlink written 8.9 years ago by Lars Juhl Jensen11k
1
gravatar for Science_Robot
8.9 years ago by
Science_Robot1.1k
Gainesville, FL
Science_Robot1.1k wrote:

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'.

ADD COMMENTlink modified 3 months ago by RamRS25k • written 8.9 years ago by Science_Robot1.1k
1
gravatar for Alexandra Louis
8.9 years ago by
Alexandra Louis10 wrote:

what about integr8 at the ebi? http://www.ebi.ac.uk/integr8/FtpSearch.do?orgProteomeId=23 all the proteome set is available.

ADD COMMENTlink written 8.9 years ago by Alexandra Louis10
0
gravatar for Marina Manrique
8.9 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

I'd do this. using the advanced search

  1. Search by organism "Helicobacter pylori 26695"
  2. And then search by keyword = Complete proteome

Here you can find more info about what "Complete proteome" keyword means

ADD COMMENTlink modified 11 days ago by RamRS25k • written 8.9 years ago by Marina Manrique1.3k
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