Dear Biopythoneers, Biopython 1.74 has been released and is available from our website and PyPI. This release of Biopython supports […]
One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. […]
Due to a huge influx of spam across all OBF wikis, we are in the process of locking down new […]
After 10 years of development, the BioRuby paper is finally published in the Bioinformatics journal. The article is open access, […]
BioPerl has migrated to git and GitHub! We have also set up a mirror set of several key repositories at the […]
In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores […]
One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) […]
I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the […]
This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ […]
BioPerl 1.6.1 is now available for ActivePerl as a PPM, instructions for downloading can be found on the BioPerl wiki. […]
We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can […]
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 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.
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.
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.
Hi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea […]
An Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics. An advance copy of […]