Bioperl: 0.05 pre release

Ewan Birney
Fri, 19 Mar 1999 19:10:32 +0000

   Bioperl pre release 0.05

Bioperl is getting close to making a stable branch (0.05) with the new
code which has come in since novemeber last year. To try to persuade
people to pick up the code and try it out, I've made a pre-release
as a CPAN'able tar distribution.

It is up at

as bioperl-0.05.pre.tar.gz

After download

	perl Makefile.PL
        make test

to make and test the package. Examples gives you some examples
to play with.

The aim is to get as many people as possible hammering the new
version before we make the stable branch in the CVS repository
(once we do that, we only make bug fixes down the branch).

The more you test it now, the better it will be, so please give
it a go. ;)

The 0.05 release will have the following new features (all
of which are in and pass tests in the pre release).

    o New, sleaker BLAST parsing code from Steve Chervitz. Though
not entirely solving the memory usage problem

    o http database mounting by Aaron Mackay. Using this GenBank and GenPept
can be accessed from NCBI directly using http calls

    o flat file indexing from James Gilbert for Fasta file sequence
databases and from Ewan Birney for EMBL .dat files

    o Signal Peptide prediction from Chris Dagdigian

    o A new, cleaner SeqIO system for sequence formats, with fasta, embl,
raw supported at the moment.

    o Experimental support for Sean Eddy's Extreme Value Distribution
fitting code via a C/Perl interface.

    o Lots of bug fixes ;)

Please - mail your thoughts about it back to the perl guts list

Ewan Birney

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