Bioperl: Bioperl 0.6 Released
Tue, 4 Apr 2000 10:44:36 +0000 (GMT)
Announcing bioperl 0.6 release
The bioperl developers are delighted to announce the bioperl 0.6
release. The 0.6 release is the latest stable release, replacing the
old 0.05.1 release. Bioperl is coordinated from http://bio.perl.org.
Please visit the web site for more details about the project
The release is available from
as a set of CPAN modules (bioperl-0.6.tar.gz and bioperl-ext-0.6.tar.gz)
The releases are also available from CPAN. Please check out your
nearest CPAN mirror site (http://www.cpan.org/ for the top level).
The bioperl-0.6 is the main distribution. The bioperl-ext is an
additional distribution with compiled C extensions. bioperl-ext is not
needed for the majority of the functionality of bioperl-0.6.
The installation process is a standard CPAN module, requiring the commands
(make test - optional)
The README has more details on this.
The 0.6 release as the following new or improved functionality:
o Sequences can have Sequence Features attached to them
- The sequence features can be read from or written to
EMBL and GenBank style flat files
o Objects for Annotation, including References (but not
full medline abstracts), Database links and Comments are
o A Species object to represent nodes on a taxonomy tree
o The ability to parse HMMER and Sim4 output has been added
o The Blast parsing has been improved.
o Flat file indexed databases provide both random access
and sequential access to their component sequences.
o A CodonTable object has been written with all known
o A number of new lightweight analysis tools have been
added, such as molecular weight determination.
The 0.6 release also has improved software engineering
o The sequence objects have been rewritten, providing more
maintainable and easier to implement objects. These
objects are backwardly compatible with the 0.05.1 objects
o Many objects are defined in terms of interfaces and then
a Perl implementation has been provided. The interfaces
are found in the 'I' files (module names ending in 'I').
This means that it is possible to wrap C/CORBA/SQL access
as true "bioperl" objects, compatible with the rest of
o The SeqIO system has been overhauled to provide better
processing and perl-like automatic interpretation of <>
o Many more tests have been added (a total of 172 automatic
tests are now run before release).
Comments, praise or annoyances should be directed to the
bioperl-guts list (firstname.lastname@example.org).
Bugs should be entered through the bug tracking interface
found at http://bio.perl.org/bioperl-bugs/.
Ewan Birney (on behalf of the bioperl developers).
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