[Biococoa-dev] Digest tool

[Alexander Griekspoor]

>> The trick I use for recognizing sites with ambiguous bases here comes 
>> from the use of strings – I simply call a method that builds up an 
>> array of all possible sequences, then search for each of them.  For 
>> N’s, I count how many there are and just skip forward that many 
>> bases.
>
> In my current code, I also use strings to scan for the characters 
> representing the cleavage sites. When we decide on using the BCScanner 
> class, we should be able to scan a symbolArray directly. So no need 
> for a sequence -> string -> sequence conversion which will speed 
> things up.

Hooray, yes I would love to see a BCScanner (obviously ;-)
Alex

**************************************************************
                         ** Alexander Griekspoor **
**************************************************************
                  The Netherlands Cancer Institute
                  Department of Tumorbiology (H4)
             Plesmanlaan 121, 1066 CX, Amsterdam
                        Tel:  + 31 20 - 512 2023
                        Fax:  + 31 20 - 512 2029
                       AIM: mekentosj at mac.com
                       E-mail: a.griekspoor at nki.nl
                    Web: http://www.mekentosj.com

MacOS X: The power of UNIX with the simplicity of the Mac

***************************************************************