Re: [Seqan-dev] seqan
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:
