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

[Robert Bradbury]

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