Biopython

Dear biopythoneers, We are pleased to announce the release of Biopython 1.42. This release includes a brand-new Genbank parser in Bio.GenBank by Peter Cock, numerous updates to Bio.Nexus by Frank Kauff and to Bio.Geo by Peter, lots of bug fixes by scores of contributors through BugZilla, and Bio.Cluster became object-oriented. Source distributions and Windows installers are available from our spiffy new Wiki-based website at http://biopython.org. My thanks to all code contributors who made this new release possible. [Read More]

We are pleased to announce the release of Biopython 1.41. Many improvements were made in Biopython during the eight months since the previous release, and the new release contains lots of bugfixes, improvements, new functionalities, and better documentation. To pick a few, there’s the new Bio.MEME module by Jason Hackney, updates to the Blast parser using Bertrand Frottier’s NCBIXML code, a BLAT parser by Yair Benita, numerous updates in Bio.PDB, CompareACE support in AlignAce, and improved user-friendliness in Bio. [Read More]

We are pleased to announce the release of Biopython 1.40 beta. It has been nine months since the last official release (1.30), and there are numerous changes, bugfixes, enhancements, goodies and new contributors. Most notable are the addition of the Nexus parser (Frank Kauff w/ Cymon Cox), the CAPS module (Jonathan Taylor), the Restriction enzyme package (Frederic Sohm), hefty improvements to Bio.PDB (Thomas Hamelryck), MutableSeq (Michiel de Hoon), and more. The delay in the release was caused by day jobs creeping into the lives of most core developers. [Read More]

I’m happy to announce a new release of Biopython 1.30, available today from http://biopython.org. This release contains a number of new modules and substantial changes to older modules. As a result of the changes, we’ve bumped up to a brand new major number. Please do download, test with your code, and report any bugs or problems to the normal lists (biopython at biopython.org or biopython-dev at biopython.org). For the full details about changes, please see: http://portal. [Read More]

I’m happy to announce the 1.24 release of Biopython. As normal Biopython is available from http://biopython.org. The major changes in this release, in addition to the usual bug fixes, are: New parsers for Phred and Ace format files – thanks to Frank Kauff New Code for dealing with NMR data – thanks to Bob Bussell New SeqUtils modules for codon usage, isoelectric points and other protein properties – thanks to Yair Benita New code for dealing with Wise contributed by Michael EZ-Retrieve sequence retrieval now supported thanks to Jeff Bio. [Read More]

Jeff announces a new release of Biopython: Biopython 1.23 is now available from the website at: http://www.biopython.org/ This is mostly a maintenance release, which fixes some problems in the installation. You do not need to update from 1.22 unless you are using the Bio.Cluster, Bio.KDTree, or Bio.PDB.mmCIF packages. The changes made in this release are: Fixed distribution of files in Bio/Cluster Now distributing Bio/KDTree/_KDTree.swig.C minor updates in installation code added mmCIF support for PDB files [Read More]

Available now at http://biopython.org/download/ Changes include: added Andrew Dalke’s EUtils library added Michiel de Hoon’s gene expression analysis package updates to setup code, now smarter about dependencies updates to test suite, now smarter about code that is imported Michael Hoffman’s fixes to DocSQL syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible updates in NCBIStandalone, short query error Sebastian Bassi submitted code to calculate LCC complexity Greg Kettler’s NCBIStandalone fix for long query lengths slew of miscellaneous fixes from George Paci miscellaneous cleanups and updates from Andreas Kuntzagk Peter Bienstman’s fixes to Genbank code – now parses whole database Kayte Lindner’s LocusLink package miscellaneous speedups and code cleanup in ParserSupport by Brad Chapman miscellaneous BLAST fixes and updates Iddo added new code to parse BLAST table output format Karl Diedrich’s patch to read T_Coffee files Larry Heisler’s fix for primer3 output Bio. [Read More]

Do you need to access sequences from multiple places? Would you like to easily retrieve your own local sequences from indexed flat files, all other sequences on species X from department wide raletional database and the rest from global internet servers? The Open Biological Database Access (OBDA) System was designed so that one could use the same application code to access data from all three of the database types by simply changing a few lines in a “configuration file”. [Read More]