How to find a random set of proteins which are not in your target set?
2
0
Entering edit mode
4.2 years ago
mcc ▴ 80

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.

ncbi protein random search null set • 1.2k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
3
Entering edit mode
4.2 years ago
mcc ▴ 80

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4.2 years ago
Bioaln ▴ 350

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

ADD COMMENT

Login before adding your answer.

Traffic: 1816 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6