Dear Biopythoneers, Biopython 1.74 has been released and is available from our website and PyPI. This release of Biopython supports […]
Biopython 1.74 released
July 16th, 2019 by PeterChromosome Diagrams in Biopython
October 28th, 2011 by PeterOne 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 wikis
March 17th, 2011 by Chris FieldsDue to a huge influx of spam across all OBF wikis, we are in the process of locking down new […]
BioRuby paper published
August 26th, 2010 by Naohisa GotoAfter 10 years of development, the BioRuby paper is finally published in the Bioinformatics journal. The article is open access, […]
BioPerl has moved to GitHub
May 14th, 2010 by Chris FieldsBioPerl 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 Indicator
April 30th, 2010 by PeterIn 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 easier
April 5th, 2010 by PeterOne 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 variants
December 17th, 2009 by PeterI’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 Biopython
December 14th, 2009 by PeterThis 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 available
October 10th, 2009 by Chris FieldsBioPerl 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 released
September 29th, 2009 by Chris FieldsWe 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 matters
September 25th, 2009 by PeterBiopython’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 migration
September 24th, 2009 by PeterBiopython 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 Biopython
September 22nd, 2009 by davidwIn 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 Biopython
September 21st, 2009 by PeterThe 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 PeterConstructing 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 Cookbook
April 29th, 2009 by davidwHi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea […]
Biopython paper published
March 22nd, 2009 by Iddo FriedbergAn Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics. An advance copy of […]