Re: [Seqan-dev] seqan

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Hi Sven,

have a look at the new "init_score.cpp" demo. I just committed it into trunk.

To build it, update your trunk checkout, go to your cmake directory, execute cmake again. Then, you can execute "make init_score", build it and execute it via "./demos/init_score".

You can find the source code here:

https://trac.mi.fu-berlin.de/seqan/browser/trunk/seqan/projects/library/demos/init_score.cpp

The demo shows how to initialize the matrix using one of the built-in static matrices, how to define your own static matrix and how to initialize it by setting the values manually.

HTH
*m

Am 02.08.2010 um 13:14 schrieb Sven Nahnsen:

> 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:
>> 
>> 
>