[Bioperl-l] Classifying SNPs

[Chris Fields]

Bio::Coordinate might help with coordinate conversion.  However, much  
of this sounds very Ensembl-like.  Have you looked at the Ensembl perl  
API?  It can do #1 (coordinate conversion), and I'm sure something  
could be written up to do the second.

chris

On Jul 13, 2009, at 10:43 AM, Mark A. Jensen wrote:

> Thanks Abhi-- I had a feeling there was more (or "less") to it--  
> this would be a nice feature to have, don't think it exists. Will  
> think about it-- cheers
> ----- Original Message ----- From: "Abhishek Pratap" <abhishek.vit at gmail.com 
> >
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Cc: <bioperl-l at lists.open-bio.org>
> Sent: Monday, July 13, 2009 11:10 AM
> Subject: Re: [Bioperl-l] Classifying SNPs
>
>
>> Dear Mark
>> Sorry I was not able to reply earlier. Many Thanks for your detailed
>> explanation. However this is not exactly what I am looking for. May  
>> be my
>> initial mail was not well articulated or I am not able to infer  
>> your reply
>> fully. My bad.
>>
>> Well as an input what we have is the just the genomic coordinates  
>> for SNP's
>> predicted by Illumina propriety software CASAVA. What we would like  
>> to do is
>> to further classify these predicted SNP's  . If they fall into  
>> Coding region
>> then whether they are synonymous/non-syn SNPs.
>>
>> So I guess something which translates
>> 1. SNP genomic coordinate into mRNA offset
>> 2. Then identify the ORF and target codon and check whether the SNP
>> substitution will be syn/non-syn.
>>
>> Thanks,
>> -Abhi
>>
>> On Wed, Jul 8, 2009 at 11:23 AM, Mark A. Jensen <maj at fortinbras.us>  
>> wrote:
>>
>>> Hey Abhishek-
>>> You might root around in Bio::PopGen. Here's a script to get stuff  
>>> from
>>> raw fasta data--see comments within.
>>> cheers
>>> Mark
>>>
>>> use Bio::AlignIO;
>>> use Bio::PopGen::Utilities;
>>>
>>> $file = "your_raw_file.fas";
>>>
>>>
>>> my $aln = Bio::AlignIO->new(-format=>'fasta', -file=>$file)- 
>>> >next_aln;
>>> # get the alignment into a Bio::PopGen::Population format, with  
>>> codons
>>> # as the marker sites
>>> my $pop = Bio::PopGen::Utilities->aln_to_population(-alignment=> 
>>> $aln,
>>> -site_model=>'cod');
>>> # here are your variable codons...
>>> my @cdnpos = $pop->get_marker_names;
>>> # here are your individuals represented in the alignment
>>> my @inds = $pop->get_Individuals;
>>> # which have names like "Codon-3-9", "Codon-4-12", etc
>>> foreach my $cdn (@cdnpos) {
>>>  # calculate the unique codons represented at this codon position
>>>  my (%ucdns, @ucdns);
>>>  @genos = $pop->get_Genotypes(-marker=>$cdn);
>>>  $ucdns{$_->get_Alleles}++ for @genos;
>>>  @ucdns = sort keys %ucdns;
>>>  #
>>>  # here, use translate or something faster to identify syn/non-syn
>>>  # check out code in Bio::Align::DNAStatistics for various methods
>>>
>>> }
>>> # relate back to individuals with this
>>> foreach my $ind (@inds) {
>>>  print "Individual ".$ind->unique_id."\n";
>>>  print "Site\tAllele\n";
>>>  foreach my $cdn (@cdnpos) {
>>> print $cdn, "\t", $ind->get_Genotypes($cdn)->get_Alleles, "\n";
>>>  }
>>> }
>>>
>>>
>>> 1;
>>>
>>> ----- Original Message ----- From: "Abhishek Pratap" <
>>> abhishek.vit at gmail.com>
>>> To: <bioperl-l at lists.open-bio.org>
>>> Sent: Wednesday, July 08, 2009 10:24 AM
>>> Subject: [Bioperl-l] Classifying SNPs
>>>
>>>
>>>
>>> Hi All
>>>
>>> This might seem to be an old track question. However I was not  
>>> able to
>>> find a good answer in the many diff mailing list archives.
>>>
>>> For all our SNP predictions we would like to know whether they are
>>> synonymous / non-synonymous. If Non-synonymous/Exonic then find the
>>> position on the gene where amino acid is getting changed and to what
>>> ...Also info about indels will help.
>>>
>>> I am not sure if something like this already exists. If not even  
>>> some
>>> pointers on how to move forward will help.
>>>
>>> Thanks,
>>> -Abhi
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
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