[Biococoa-dev] BioCocoa 2.1.0 release

Scott Christley schristley at mac.com
Fri Oct 3 23:25:23 EDT 2008


A new release of BioCocoa is now available; download is available from  
the BioCocoa website  Below is some news about what is available.  If  
you feel all excited and want to broadcast this all around, I ask to  
maybe consider holding off for the moment :-)

Part of this is a run-through to document all the steps required to  
make a release, this will help in making periodic consistent releases  
in the future.  For that purpose, it would be much more helpful if  
people downloaded and prodded it and send back any comments.  There  
are some things definitely missing, most notably example programs to  
show off the library, and who knows what else.  This will give me a  
chance to walk through the process a few times, and hopefully we will  
have a true release soon!



BioCocoa 2.1.0 -- (found in Tags / 2.1.0)

- New BCSuffixArray and BCMCP classes for constructing disk-based  
suffix arrays of sequences and finding the maximum common prefixes of  
sequences using those suffix arrays.  This is work based upon the  
following publication:

	Scott Christley, Neil F. Lobo and Greg Madey.
	Multiple Organism Algorithm for Finding Ultraconserved Elements.
	BMC Bioinformatics, 9: 15, 2008.

- New BCCachedSequenceFile and BCCachedFastaFile classes that allow  
for reading sequence data without reading the whole sequence into  
memory.  This is useful for working with very large sequences like  
whole genomes.  A future release will support a BCCachedSequence which  
provides a consistent sequence interface regardless of whether the  
sequence is in memory or cached on disk.
- File format can be explictly provided to BCSequenceReader using  
- Documentation updates.
- More complete port to GNUstep, all BCFoundation functionality should  
be available.
- Quad-fat binary supporting 32/64-bit and ppc/intel processors.

More information about the Biococoa-dev mailing list