[Bioperl-l] store variations, generate sequences

[Marian thieme]

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