[Bioperl-l] store variations, generate sequences

Albert Vilella avilella at gmail.com
Tue Jan 2 12:35:58 EST 2007


The Bio::PopGen modules contain Individual, population and genotype
objects, among other utilities. There are some input/output formats in
Bio::PopGen::IO and also some methods to go from an aln to a
population.

That said, I am not entirely sure about how much of that overlaps with
Bio::Variation.

If you think anything missing that you would like to have implemented
in bioperl, we would greatly appreciate your feedback,

Cheers,

    Albert.

On 1/2/07, Marian Thieme <marian.thieme at klinik.uni-regensburg.de> wrote:
> 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
>
> --
> Marian Thieme
> University Regensburg
> Institute of Functional Genomics
> Josef-Engert-Str. 9
> 93053
> Regensburg
> Germany
> P: 0049 (0)941 943 5055
> F: 0049 (0)941 943 5020
> E: marian.thieme at klinik.uni-regensburg.de
> W: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik
>
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