Help with verifying that I'm looking at polymorphisms? - (Jan/06/2012 )
Sorry that I couldn't think of a better sounding title!
Basically I've had to do some Bioinformatic work recently having never ever done or even heard of the subject before, so I'm a complete novice as to how to use all the websites like NCBI, Vega Sanger, BLAST, BLAT... etc.! and I'm finding it really hard to understand exactly what it is that I'm looking at.
I've been trying to find the number of polymorphisms in a particular gene, human TRIM5. I found one website with it on http://www.uniprot.org/uniprot/Q9C035 and simply counted the 'Natural Variants' to come up with a number of 10. However, I would be really grateful if anybody could give me some guidance. Are these natural variants actually the same as polymorphisms? Have I actually managed to include all of the polymorphisms (if they are indeed 'natural variants') or am I accidentally only looking at a subset of polymorphisms?
Just to re-iterate the fact that I really feel out in deep water with this subject and so if you do give any answers please feel free to phrase any reply as if I'm a little bit stupid! I really want to understand what all these things are, feeling lost is a very horrible feeling!
Any help would be MUCH appreciated.
Thanks in advance!
Technically (or so I was taught) a polymorphism is a mutation that is propagated and forms part of a stable system (i.e. a percentage of the population would naturally carry the mutation). This does not mean that these are the only mutations possible (technically any base-pair can be changed, which may or may not result in an amino acid change). The natural variants are the same as polymorphisms.
The polymorphism listed on websites are only those found so far.
So it sounds like I probably have counted correctly and considered the right things. Major relief!
Thanks so much for your reply
Well I would be more cautious with the "natural variant". I looked up one gene I'm working with on Uniprot, and found two published pathological mutations marked there as natural variant. That wouldn't clasify as a polymorphism.
Also several other known polymorphisms (present in healthy population and/or having no known efect on enzyme function) weren't even present.
Only database that should contain all polymorphisms and known variants (even disease causing) is dbSNP. That contains nucleic acid polymorphisms that doesn't change protein sequence and those that does.