|Interface||Command line interface|
|Restrictions to use||None|
|Requirements||matplotlib, Graphviz, NetworkX|
Add your version
- Documentation: http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
- person_outline Eric Talevich <>
- person_outline Biopython Team <>
[…] the alignments that overlap the mouse peak and include hg19 were extracted. we calculated the human mouse pairwise alignment for each multiple alignment using the “globalms” function of biopython (http://biopython.org/, version 1.59; python version 2.71). the highest scoring pairwise alignment formed base of the orthologous region in human. this region was extended on either side […]
[…] reads across the collection, reads were mapped to the accessory genome component using bwa v0.7.3 . the coverage plots were then generated using samtools . heatmaps were generated using biopython ., wph has consulted for glaxosmithkline. kpk has consulted for pfizer, glaxosmithkline and merck. kgk has an investigator-initiated study sponsored by glaxosmithkline. sdb […]
We use Biopython mainly for standard formats (Genbank/Fasta/AB1) import/export, and for basic restriction/ligation simulations. For more advanced uses we generally need to build a functionality on top of Biopython, or use an existing library that does that.
One downside of Biopython is the presence of many sub-packages from different subdomains of bioinformatics, which makes the library very big and hard to navigate (also hard to fully maintain I imagine).