I’ve just finished writing up an example for the Biopython Tutorial of the new GenomeDiagram functionality added in Biopython 1.59. […]
One of the new things coming in Biopython 1.59 is improved chromosome diagrams, something you may have seen via Twitter. […]
In another quirk to the FASTQ story, recent Illumina FASTQ files don’t actually use the full range of PHRED scores […]
This is another blog post to highlight one of the neat tricks you’ll be able to do with Biopython 1.54 […]
This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ […]
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.
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 […]
I updated the Trees HowTo with some code demonstrating how to automatically generate postscript trees from newick or nexus tree […]