[Biojava-l] Uppercase/lowercase sequences

mark.schreiber at group.novartis.com mark.schreiber at group.novartis.com
Tue Feb 3 19:47:22 EST 2004


There has been some talk of changing that in future versions of biojava. 
However you may be able to get the desired behaivour by making your own 
SymbolTokenizer and making it case sensitive. In this way you can map 
lower or upper case characters to any Symbol you want. You could even go 
as far as making your own Alphabet.

It really depends on what you wish to do with these soft masked sequences.

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
1 Science Park Road
#04-14 The Capricorn
Singapore 117528

phone +65 6722 2973
fax  +65 6722 2910

Maik Hassel <mhassel at bcgsc.bc.ca>
Sent by: biojava-l-bounces at portal.open-bio.org
02/04/2004 07:27 AM

        To:     biojava-l at biojava.org
        Subject:        [Biojava-l] Uppercase/lowercase sequences

Hello everybody!

I saw some postings about this topic already on the list, but no "real" 
solution so far.
I take it that seqeunces are always handled in lowercase letters, so 
that basically biojava is unsuitable for working together with any 
algorythms that use soft masked sequences.

Is there any plan to actually change that in the near future, or is 
there already a solution that I missed?

Thanks for any comments

P.S: When replying, please please please cc directly to me, too!

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