[BiO BB] how to search genes around certain SNP

[Mike Marchywka]

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> Date: Mon, 12 Apr 2010 13:15:45 +0300
> From: pj.siivola at luukku.com
> To: bbb at bioinformatics.org
> Subject: [BiO BB] how to search genes around certain SNP
>
> Hi!
>
> I would be interested to find out genes around spesific SNPs (genes which are ~ 1 MB away from SNP or less). What would be most efficient way to do this ? Suggestions?
>

You want annotated genome or you want to query a gene DB by location ( proximity to your SNP) or actually plow through DNA near your SNP?
I haven't tried it but something like this may help, probably lets
you play with annotated genomes and your own data, 
http://www.ncbi.nlm.nih.gov/projects/gbench/
 
 
I don't know if anyone answered the latter cases but you can download 
gene DB or genomes themselves for more efficent access and specialize
the local storage format to your immediate needs ( this all takes
time but if you really care about efficient usage it can produce benefits).  
In the past I've done similar things by requsting large junks of adjcent genome from the relevant
database at ncbi. I guess efficient depends on usage however. If you do 
this a lot, and if you really care about efficiency, 
it may be faster to get a local copy of your targets genome
and put into a DB of your choice. "DB" could just be a bunch of flat 
files and use some simple compressed format with chunk sizes that give
you reaonable "random access" performance. For example, name files something like ChromoX_start_N_end_M.zip and then load/unzip the one or two that have the  relevant data. Simple content specialized compression ( like
changing 8 bit chars into 2( Although IIRC this has problems for 
placeholders for missing data, there may be other issues on which someone could comment ) may improve performance( even if you have plenty of disk space, transfer and memory acceses may be faster if the data is smaller).
 
Does this address your need?
 
 
 
 
>
> Thanks in advance!
>
> Päivi Rosenström
> 		 	   		  
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