How To Get A Full Proteome Of Helicobacter Pylori 26695.

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

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updated 15.5 years ago by Marina Manrique

• written 15.5 years ago by Marcinmagnus •

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

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updated 6.9 years ago by Ram

• written 15.5 years ago by Marcinmagnus •

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

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written 15.5 years ago by Marina Manrique

4 answers

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).

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written 15.5 years ago by Lars Juhl Jensen

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?

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updated 6.9 years ago by Ram

• written 15.5 years ago by Marcinmagnus •

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

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updated 6.9 years ago by Ram

• written 15.5 years ago by Jerven •

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.

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written 15.5 years ago by Lars Juhl Jensen