[Bioperl-l] store variations, generate sequences
marian.thieme at lycos.de
Tue Jan 2 11:57:04 EST 2007
sorry if you get this email twice, prob. the first time I have used the
wrong sender address
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
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:
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;
my $a2 = Bio::Variation::Allele->new;
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 ?
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