Question: How to find a random set of proteins which are not in your target set?
0
gravatar for mcc
9 months ago by
mcc80
PVD, USA
mcc80 wrote:

I am seeking a way to download a random set of >600 proteins from NCBI (for example) that are NOT my target protein set. For example, I have a list of fasta files which are hemoglobin, myoglobin (all available species) and want to find fasta files that do NOT contain these proteins. I am seeking this 'null set' of proteins for comparison.

Forgive me, this might be similar to another question but I could not seem to find the proper key words for my search.

ADD COMMENTlink modified 9 months ago by Bioaln250 • written 9 months ago by mcc80

All the Entrez sites support standard boolean queries. It's a bit 'hacky' but you could simply search the protein databases for something like "NOT haemoglobin". I'm not sure if this will work without something to compare the intersection to, but give it a try.

ADD REPLYlink modified 9 months ago • written 9 months ago by jrj.healey4.2k

Hi jrj, Yes i tried that early on and it did not work. However, Searching around Biostars I found (how can I combine uniprot's random and limit functionality?) which I had seen before...

ADD REPLYlink written 9 months ago by mcc80
3
gravatar for mcc
9 months ago by
mcc80
PVD, USA
mcc80 wrote:

UniProt Random Sequence Picker
http://www.rocrooks.co.uk/biology/uniprot-random.php

ADD COMMENTlink written 9 months ago by mcc80

Cool. Had no idea that's the sort of thing people would have found a need for!

ADD REPLYlink written 9 months ago by jrj.healey4.2k
0
gravatar for Bioaln
9 months ago by
Bioaln250
France
Bioaln250 wrote:

If you have IDs for individual proteins, simply take the difference between them, and all others and download the FASTAs.

ADD COMMENTlink written 9 months ago by Bioaln250
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