Re: [Seqan-dev] seqan

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

Whoops, I guess the HTTPS site is password protected

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

Access should be public there.

*m

Am 02.08.2010 um 13:46 schrieb Holtgrewe, Manuel:

> 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:
>>> 
>>> 
>> 
>