Re: [Seqan-dev] seqan

[Sven Nahnsen <nahnsen@informatik.uni-tuebingen.de>]

Hi Manuel,

I work with OpenMS and I use some SEQAN funtionality to score pairwise 
sequence alignments of peptides.
This works nicely while using your predefined matrices, such as Blosum62 
or the PAM matrices.

I use the following code:
/////////////////////////////
::seqan::Align<TSequence, ::seqan::ArrayGaps> align;
::seqan::resize(rows(align), 2);
::seqan::assignSource(row(align, 0), seq1);
::seqan::assignSource(row(align, 1), seq2);
::seqan::Score<int, ::seqan::Pam<> > pam(PAM, -opening_penalty, 
-extension_penalty);
c = (DoubleReal)globalAlignment(align, pam,::seqan::NeedlemanWunsch());
///////////////////////////

However I would like to use a slightly modified PAM matrix (PAM30MS), 
that is specifically designed for my purposes.
From your documentation I so far couldn't figure out how to initialize 
the entries of a new (24x24) matrix.

Thanks for your help!

Best,

Sven




On 02.08.2010 12:44, Holtgrewe, Manuel wrote:
> Hi Sven,
>
> Ich beantworte deine Frage gerne. Stell die ganze Frage und was du genau machen willst doch mal an die SeqAn Mailing Liste
>
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
> Dann haben alle die im Archiv nachsehen was davon ;)
>
> *m
>
> Am 02.08.2010 um 12:40 schrieb Chris Bielow:
>
>