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Re: Re: st: New program - snpgrab


From   Elwood Cook <danielecook@gmail.com>
To   statalist@hsphsun2.harvard.edu
Subject   Re: Re: st: New program - snpgrab
Date   Wed, 1 Feb 2012 10:22:42 -0600

Hello,

I have updated snpgrab, a program to retrieve snp data from dbSNP and
written two additional programs which interact with NCBI efetch
utilities. I changed the name to snpfetch (from snpgrab) and also have
now written the following:

snpfetch - Used to retrieve information on a set of snps (changed name
from snpgrab)
genefetch - Used to retrieve infromation on a set of genes from Names or IDs
pmidfetch - Used to retrieve information on a set of publications based on pmid

You can install the files here by typing the following:

net from http://www.elwoodcook.com/stata/

Please provide any comments/feedback you may have.

Thanks,
-E




On Mon, Jan 30, 2012 at 8:02 PM, Airey, David C
<david.airey@vanderbilt.edu> wrote:
> .
>
> SNPs or single nucleotide polymorphisms are nucleotide (A,G,C,T) substitutions in our DNA, resulting in the potential for altered amino acid sequence in proteins and changes in their functions. It sometimes results in no change, sometimes in a change, because the DNA code is degenerate. More than one sequence of 3 nucleotides (a codon) can map to a single amino acid. SNPs are one kind of genetic polymorphism that contribute to individual differences normal and abnormal physiology. Anyway, as you might imagine, known SNPs in our DNA are not named willy-nilly. A lot of effort has been put into being able to look up a given SNP and know what it is. More about naming SNPs can be read at NIH.gov. Those who might find Elwood's program of use would have no complaints about the naming of SNPs that I can think of, but a help file would be welcome. Generally, you might have a list of SNPs from some other source, and you quickly want to get additional information about each SNP from !
 an!
>  online resource, such as dbSNP or BioMart (what location on what chromosome, maybe if it is located in a given gene's coding or promoter region, etc.).
>
> I have found looking at his program useful to learn how to use some of Stata's commands I don't use.
>
> -Dave
>
>
>> I trust that is an explanation for people working in the field.
>> Perhaps what such people do is start with an empty dataset and then
>> read in data and -snpgrab- uses more or less predictable names for
>> different variables.
>>
>> It's not good practice in general that programs should make too many
>> presumptions about what names are, or are not, in use.
>>
>> I imagine your help file will clarify these matters.
>>
>> Nick
>
>
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-- 
-E

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