[BioC] Distinguish Synonymous vs. Non-synonymous SNPs

[michael watson (IAH-C)]

I'm not sure BioC is the tool you want to use.

Have you tried something like BioPerl:

http://www.bioperl.org/Core/Latest/bioscripts.html#scripts_utilities_pairwise_kaks_pls

"Takes DNA sequences as input, aligns them as proteins, projects the alignment back into DNA and estimates the Ka (non-synonymous) and Ks (synonymous) substitutions."
________________________________________
From: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wu, Xiwei [XWu at coh.org]
Sent: 29 January 2010 17:26
To: Michael Dondrup
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Distinguish Synonymous vs. Non-synonymous SNPs

Michael,

Thanks a lot for your help. I will give it a try. Is it good for novel
SNPs not in the dbSNP? The SNPs I got are from a sequencing project,
many of them are not in dbSNP.

Xiwei

-----Original Message-----
From: Michael Dondrup [mailto:Michael.Dondrup at uni.no]
Sent: Friday, January 29, 2010 3:11 AM
To: Wu, Xiwei
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Distinguish Synonymous vs. Non-synonymous SNPs

Hi Xiwei,
do you mean SNPs that result in non-synonymous vs  synonymous coding?
Then a biomart query might do the
job and therefore the package biomaRt could be used to query from within
R.  There is a filter in biomart for different
consequence types of SNPs, one of which is NON_SYNONYMOUS_CODING. You
can check which filter seems appropriate
This lengthy Url represents a possible query in the biomart web
interface:

http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIB
UTES=hsapiens_snp.default.snp.refsnp_id|hsapiens_snp.default.snp.chr_nam
e|hsapiens_snp.default.snp.chrom_start|hsapiens_snp.default.snp.conseque
nce_type_tv|hsapiens_snp.default.snp.ensembl_type|hsapiens_snp.default.s
np.ensembl_peptide_shift|hsapiens_snp.default.snp.phenotype_description|
hsapiens_snp.default.snp.phenotype_name&FILTERS=hsapiens_snp.default.fil
ters.consequence_type."NON_SYNONYMOUS_CODING"&VISIBLEPANEL=resultspanel


it should be possible to set identical parameters in the bioconductor
package biomaRt although I didn't try this yet.

Best
Michael


Am Jan 29, 2010 um 1:57 AM schrieb Wu, Xiwei:

> Dear list,
>
> I have a list of SNPs with chromosome location, and trying to see
which
> ones are non-synonymous. Are there any packages/functions that can
> distinguish synonymous and non-synonymous SNPs? I tried to search the
> list, but could not find anything related. Thanks in advance.
>
> Xiwei
>
>
>
>
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