Re: [Seqan-dev] extendSeed for protein sequences

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

On 08.11.2011 01:54, Beifang Niu wrote:
> Hi all,
>
> There is one example for DNA seed extension in the seqan tutorial. If I
> want to do the seed extension for protein sequences using blosum 62
> scoring matrix.
> How to do it?  Can I directly use extendSeed function?  It seems that
> the score parameter of the extendSeed function is simple score type. Can
> I use blosum 62 scoring matrix for extendSeed function?
>
> thank you,
> Beifang.
Beifang,

the tutorial gives the following for using simple score matrices:

    typedef int TScore;
    Score<TScore, Simple> scoreMatrix(1, -1, -1);
    TScore scoreDropOff = 1;
    extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2, 
GappedXDrop());

The alignment tutorial [1] explains how to use the built-in Blosum 62. 
You can also find Blosum62, other Blosums, Pams and Vtml200 in the 
documentation. You probably want to do the following:

    typedef int TScore;
    TScore gapExtend = -1, gapOpen = -11;
    Blosum62 scoringScheme(gapExtend/* optional:, gapOpen*/);
    extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2, 
GappedXDrop());

Finally, the How-To [2] shows how to define your own score matrices.

I hope that this helps you. Can you tell us how we could improve the 
documentation such that you could have found this information faster? By 
the way, the Tutorial site has a search function ;)

Bests,
Manuel

[1] http://trac.mi.fu-berlin.de/seqan/wiki/Tutorial/Alignments
[2] http://trac.mi.fu-berlin.de/seqan/wiki/HowTo/WorkWithCustomScoreMatrices