Hi - I was wondering if it is possible the download a random sample of proteins from a given protein database. I want to do this to compare proteins of interest to "background proteins". i.e. a control. Probably a little trickier would be to download proteins that aren't of a certain type i.e. non membrane proteins.

Has anyone done anything like this. I see in papers all the time "we used non-XXX proteins as a negative training set. " And I'd imagine something like this would be a pain to do manually.

Ideally I would not like to download entire databases, but rather do this task online.

Anyone done this sort of thing?
<p>Here are all the ~20k reviewed proteins in homo sapiens in the UniProt database:</p>

<p>http://www.uniprot.org/uniprot/?query=%28taxonomy%3A9606%29+AND+reviewed%3Ayes</p>

<p>Play around, exclude some, include non-reviewed or change organism, then click download.</p>

<p>Choose which format suits you, i.e. FASTA.</p>

<p>Here is the first one (just for fun):</p>

<pre>
<code>&gt;sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1 SV=3
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY
LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY
YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD
AGEGEN</code></pre>

<p>Then load some at random.</p>
