[Bioperl-l] guessing molecule type

[Andrea Schafferhans]

Dear bioperl developers,

Thanks a lot for the great modules you have developed!

In using the sequence objects I have come across the problem that the 
molecule type cannot always be guessed correctly if the molecule is of 
type RNA, since the sequence may contain non-standard bases that are 
best represented by an X. Wouldn't it therefore be sensible to not only 
remove all gaps from the sequence before guessing the type, but also all 
Xs?

Of course, I can change that in my local bioperl installation, but I 
thought the idea might be useful for others. -- So is anyone going to 
change this in _guess_type / _guess_alphabet (whatever the method is 
called now)?

     Cheers
         Andrea

-- 

  Dr. Andrea Schafferhans    mail: Andrea.Schafferhans@lionbioscience.com
                             fon:  +49-6221-4038-410         fax: ...-201
  Scientist                  LION Bioscience
  Structural Bioinformatics  Waldhofer Str. 98, 69123 Heidelberg, Germany
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