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How to get a list of all variants (SNPs) within a gene and 5kb immediately 5'


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#1 Celltweety

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Posted 11 June 2010 - 04:18 AM

Hello,

Could anyone explain how would u obtain all the SNPs within the gene and 5kb after 5' and 3' of same gene?
Do you use NCBI or any other site for this?

I got all the SNPs for the specific gene by using the position of the gene, but when i need the 5kb region in 5' and 3' should i consider the direction of the gene and extend both my ends with 5kb?

I used the query given in NCBI website, it works fine, but the way they ask us to extend on both the sides is wrong i think so...Here is the instructions,
Query using the gene name or symbol
Results get displayed as graphics
Get the position of the gene and chr number
SUBTRACT 5kb from the 5' and add 5kb from the 3' (I THINK THIS IS WRONG, BECAUSE WE GET THE GENE REGION DELETED THEN) :(
Query the SNP pubmed again with newly calculated regions.
ex: 8[CHR] AND 198507051:19835042[CHRPOS]


Plse help..

Thanks in advance,
Celltweety :D

#2 doxorubicin

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Posted 14 June 2010 - 06:58 PM

For mouse strains, the Jackson SNP query form is very easy to use, but you can pick 2kb or 10kb, not 5kb on either side of the gene:

http://www.informati...etch?page=snpQF

#3 Celltweety

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Posted 17 June 2010 - 12:29 AM

Hi Doxorubicin,

Thank you for the link, do you know some link for human?


Celltweety

#4 dtae

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Posted 14 August 2010 - 10:51 AM

UCSC Genome browser might be helpful.

Hi Doxorubicin,

Thank you for the link, do you know some link for human?


Celltweety






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