Hi,
I'm trying to use the Meme class in org.biojava.bio.program. Currently I
write an application that will perform Meme analysis (to find conserved
motifs in DNA). I had written the application such that it will read a
fasta format file containing multiple fasta sequences. It runs fine but
the "p
Hi,
I looked to Biojava to train an HMM given a FASTA alignment file and
then use the HMM to generate 'new' sequences similar to the ones in the
FASTA file. However, I run into exactly the same problem as Todd Riley
(quoted below). Also, if I - despite the training problems - try to
generate a seq
Hello,
we have a problem with the connection to a BioSQL Database.
When we start our application for the very first time and try to connect
to the Database, it throws an SQLException "Connection is closed."
After that, when we simply repeat the process, everything works fine and
one can store S
In working with FlexibleAlignment I've found a problem. When an overlap is
empty the
underlying code in AbstractULAlignment will return nulls for positions not
containing
symbols, and this confuses things later on. An example program below will
demonstrate
a simple case of the problem (code
We had the same problem. We fixed it in a copy of biojava, but my cvs account
has been suspended. Somebody there with commit privilages that will roll our
fix back in?
Matthew
On Thursday 24 November 2005 13:51, Felix Dreher wrote:
> Hello,
>
> we have a problem with the connection to a BioSQL
It was never removed, at least not that I'm aware of. Are you using
biojava-live or biojava-1.4, or even 1.3? It should work in 1.4 and
biojava-live, or at least that's the theory. If not, then could you post
complete stacktraces for each of the two kinds of error you mention?
Note that in release
