[Seqan-dev] FW: about extendSeed of Seqan

["Kehr, Birte" <Birte.Kehr@fu-berlin.de>]

Could anyone help Beifang with the question below?

Thanks, Birte

 

 

From: Beifang Niu [mailto:neilniu.cn@gmail.com]
Sent: Montag, 7. November 2011 15:37
To: Kehr, Birte
Subject: Re: [Seqan-dev] about extendSeed of Seqan

 

Hi Birte,

 

Now I have a new question for you.

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.