Sorry - I didn't mean you personally! Because it is quite hard for me
to figure out how things are working just from the api and the
sources, I assumed it would be similar for others starting with
BioJava/BioSQL. There must be some working code around somewhere which
could be donated? Please do :-
Hi,
Thanks for your reply.
I'm using regex on SymbolLists instead of Strings, because I'm working with
large sequences stored in the memory. I think SymbolLists are more memory
efficient than Strings.
But my problem is solved now. I removed ambiguous symbols from the regex
pattern.
Regards,
Je
Hi Cor,
Thanks for your reply.
I corrected the pattern by doing the following.
When BioJava's org.biojava.bio.molbio.RestrictionEnzyme.forwardRegex()
returns the regex of a RestrictionEnzyme "gtakm" it will return
"gta[gtk][acm]". In which k (G or T) and m (A or C) are ambiguous.
So the ambiguo
Thanks - I knew it would be quite simple, as always with BioJava (once
I've figuered out how to, that is)!
Martina
Simon Foote wrote:
Hi Martina,
To add a feature to a sequence stored in a BioSQL database, all you
have to do is retrieve the sequence and then add a feature to it. The
foll
Hi all,
Is anyone working on cell modelling as for example described in the article
below (1)? And if so, is she (also) using bioJava for this and/or other open
source projects? And if so, what kind of libraries would be helpfull for
you?
Myself, I am a Java-programmer, in daily life workin
It aint biojava. Both of the screen shots look like commercial metabolic
engineering and cell modelling software.
There is a nice open source project called cellware that might be of
interest though. www.bii.a-star.edu.sg/achievements/
applications/cellware/index.asp
- Mark
"Cor Lieftink
