[Bioperl-l] how to get the protein sequences from DNA sequencesaround novel SNPs?

Mark A. Jensen maj at fortinbras.us
Mon Nov 9 16:56:24 EST 2009

I agree that BioPerl would significantly increase in value with
such a module; in fact, the BioTeam would probably buy us out.
My opinion is that the entire GWAS enterprise is the search for
such a callback function, for humans anyway. For those engaged
in this quest, if BioPerl doesn't provide a Maserati, it at least provides
good italian-made (among others) parts.
----- Original Message ----- 
From: "Robert Bradbury" <robert.bradbury at gmail.com>
To: "Guangchun Song" <gc11song at gmail.com>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Monday, November 09, 2009 4:15 PM
Subject: Re: [Bioperl-l] how to get the protein sequences from DNA 
sequencesaround novel SNPs?

> On Mon, Nov 9, 2009 at 1:08 PM, Guangchun Song <gc11song at gmail.com> wrote:
>> I'm new bioperl user.  I' working on a project: To determine the
>> status of all tutative SNPs such as non-synonymous vs. synonymous, and
>> predict the tranlational effect of non-synonymous mutations as benign
>> or malicious.  I'm trying to use bioperl to get the DNA sequence and
>> translate to protein sequence for the SNPs that are in gene's coding
>> region.  Could someone tell me how to do it?
> I too would like to know if this information is available.  I've recently
> been working with the dbSNP results from NCBI but they display the results
> in a graphical format rather than data that one can play with and ask
> questions of like "What is the most disease causing gene in the Human
> Genome?" or "What are the critical proteins damaged by gene defects in the
> Human Genome?" ... "In terms of premature deaths, extended health care
> requirements, loss of quality of life, etc.?"
> The same types of questions can be applied to the dog and cat genomes where
> there is emotional value or the cow, horse, pig, etc. genomes where there is
> economic value?
> The value of BioPerl would increase significantly if there were
> functionality that would allow easy access to "these mutations may have
> negative/positive impact" (which means you need a function that qualifies
> mutations by degree) and allow for impact to be subjectively determined
> (implying there must be some callback function to provide a user
> quality/impact rating).
> For example:
>   $/@differences =  protein_compare($mygene, $refseq_gene, @critical_aa,
> @critical_domain, $callback)
> Where $callback could "rate" differences about the protein and position and
> the "type of interest" (e.g. metal binding amino acids, structural changing
> amino acids, critical catalysis amino acids, etc.).
> A default callback would be based on some evolving definition of "critical"
> changes which result in human disease for example.
> This is a "required" capability to be able to determine things like the
> "adaptability" of a species -- those with fewest critical mutation points
> may have better adaptability to mutation increasing circumstances.
> Please pardon any errors in perl syntax/usage its been a while since I've
> written perl and I'd really rather be coding in C.
> Robert
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