[Biococoa-dev] BioCocoa 2.1.0 release
sweetcocoa at mac.com
Sat Oct 4 14:28:39 EDT 2008
Congratulations, it's really great to see that BioCocoa is alive!
On 04 Oct 2008, at 05:25, Scott Christley wrote:
> 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.
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> Biococoa-dev at bioinformatics.org
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