Dear Biopythoneers, Biopython 1.74 has been released and is available from our website and PyPI. This release of Biopython supports […]
Biopython 1.74 releasedJuly 16th, 2019 by Peter
Chromosome Diagrams in BiopythonOctober 28th, 2011 by Peter
One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. […]
Introduction of OpenID logins for OBF wikisMarch 17th, 2011 by Chris Fields
Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new […]
BioRuby paper publishedAugust 26th, 2010 by Naohisa Goto
After 10 years of development, the BioRuby paper is finally published in the Bioinformatics journal. The article is open access, […]
BioPerl has moved to GitHubMay 14th, 2010 by Chris Fields
BioPerl has migrated to git and GitHub! We have also set up a mirror set of several key repositories at the […]
Illumina FASTQ files – Read Segment Quality Control IndicatorApril 30th, 2010 by Peter
In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores […]
Making Biopython SeqIO and AlignIO easierApril 5th, 2010 by Peter
One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) […]
Sanger FASTQ format and the Solexa/Illumina variantsDecember 17th, 2009 by Peter
I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the […]
Interleaving paired FASTQ files with BiopythonDecember 14th, 2009 by Peter
This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ […]
BioPerl core 1.6.1 PPM availableOctober 10th, 2009 by Chris Fields
BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. […]
BioPerl 1.6.1 releasedSeptember 29th, 2009 by Chris Fields
We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can […]
Working with FASTQ files in Biopython when speed mattersSeptember 25th, 2009 by Peter
Biopython’s SeqIO interface revolves around SeqRecord objects which can impose a speed penalty. For FASTQ files the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing. Working directly with the raw strings is less flexible, but much faster.
Biopython CVS to git migrationSeptember 24th, 2009 by Peter
Biopython has now moved from CVS to a git repository, hosted on github.com who kindly provide git hosting for open source projects free of charge. The BioRuby project have been using github for some time, so we are in good company.
Simpler, optimized format conversion with BiopythonSeptember 22nd, 2009 by davidw
In this post we’ll look at the new convert() function that both Bio.SeqIO and Bio.AlignIO will get in Biopython 1.52. This allows easier file conversion, and internally provides a mechanism for specific optimisations, such as for FASTQ conversions.
Indexing sequence files with BiopythonSeptember 21st, 2009 by Peter
The forthcoming release of Biopython 1.52 will include a couple of nice improvements to the Bio.SeqIO module, and here we’re going to introduce the new index function.
Clever tricks with NCBI Entrez EInfo (& Biopython)June 21st, 2009 by Peter
Constructing complicated Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help. This can tell you all the searchable fields available for each of the Entrez databases.
Introducing (and expanding) the Biopython CookbookApril 29th, 2009 by davidw
Hi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea […]
Biopython paper publishedMarch 22nd, 2009 by Iddo Friedberg
An Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics. An advance copy of […]