[Bioperl-l] store variations, generate sequences

Brian Osborne bosborne11 at verizon.net
Tue Jan 2 14:06:22 EST 2007


Marian,

I can't answer your questions as I'm not familiar with these modules but in
Bioperl one place to look for example code is in the t/ directory. So I see
the following interesting files:

t/Variation_IO.t
t/SeqDiff.t
t/DNAMutation.t
t/Allele.t
t/SNP.t

This is not intended to be exhaustive, there may be other useful files in
there.

Brian O.



On 1/2/07 11:57 AM, "Marian thieme" <marian.thieme at lycos.de> wrote:

> sorry if you get this email twice, prob. the first time I have used the
> wrong sender address
> 
> Hi all,
> 
> I am quite new to bioperl and I have a question about sequence data: I
> am working on a resequencing project. Here we have resequenced 1000
> genes of a certain gene. My question: What is easiest way to store each
> discovered variation of each individual and get a fasta sequence for an
> arbitrary individual.
> 
> I would expect that there is some way to set up a reference sequence and
> store all variationsm relative to this reference sequence. Afterward it
> should be possible to genereate sequences for each indiviudal in
> question, right ?
> 
> My approach was the following:
> 
> I have created an seqdiff object:
> 
> $seqDiff = Bio::Variation::SeqDiff->new (...)
> 
> 
> and I have assigned the reference sequence to that object via:
> 
> $seqDiff->dna_ori('atgcgtatatg');
> 
> 
> Now I thought, I can create some variations via DNAMutation object:
> 
> $dnamut = Bio::Variation::DNAMutation->new (
>   -start => 6,
>   -end => 6,
>   -length => 1,
>   -isMutation => 1,
>   -upStreamSeq => 'atgcg',
>   -dnStreamSeq => 'atatg'
> );
> 
> $a1 = Bio::Variation::Allele->new;
> $a1->seq('t');
> $dnamut->allele_ori($a1);
> 
> my $a2 = Bio::Variation::Allele->new;
> $a2->seq('a');
> $dnamut->add_Allele($a2);
> 
> 
> 
> Is that the correct way to describe the reference sequence, describe a
> variation and attach this to seqdiff object ?
> Probably I didnt understand the api right. (I did assume start/end means
> start/endposition of the mutation). Is it possible to get a complete
> sequence print (fast format) of each variation/indiviudal ?
> 
> Regards,
> Marian
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