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|Interface||Command line interface|
|Restrictions to use||None|
matplotlib, Graphviz, NetworkX
No version available
- Documentation: http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
- person_outline Eric Talevich
- person_outline Biopython Team
Publications for Biopython
Profiling microbial strains in urban environments using metagenomic sequencing data
[…] sents its absence. The phylogenetic distance was calculated as the minimal total branch-length distance between leaf nodes, normalized by the total branch length, using custom python scripts based on BioPython BaseTree [, ].The phylogenetic trees were built with RAxML  version 8.1.15 (parameters: -p 1989 -m GTRCAT) and plotted with GraPhlAn . Minimum Spanning Trees were drawn with PHYLOViZ 2 [ […]
OMGene: mutual improvement of gene models through optimisation of evolutionary conservation
[…] ject home page: https://github.com/mpdunne/omgeneOperating system: Unix.Programming languages: Python v2.7.x.Other requirements: Bedtools, Exonerate, Python packages (scipy, numpy, pyfaidx, networkx, BioPython).License: GPLv3. […]
Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice
[…] iteria read quality score of ≥30, probability score of ≥0.90, and coverage ≥500.Basic statistics of total reads, and reads mapped were generated using bespoke scripts in Python including the packages BioPython and Pysam and plots drawn using Matplotlib. To compare read counts between three discrete groups the Kruskal-Wallis test was performed, and comparison over time was performed using linear re […]
Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain
[…] se of the annotation software Prokka (v1.12-beta) () with default settings, followed by a parsing of the output files for the ars operon (coding sequences) for each isolate, using the SeqIO module in Biopython () (parsing script available on request). For ars-positive isolates, a neighbor-joining tree was calculated based on concatenated sequences for arsRBC and rMLST in accordance with the proced […]
GLASSgo – Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence
[…] n a global sequence alignment (), the pairwise identity of each hit to the query sequence was computed. For performing a pairwise sequence comparison, the “pairwise2.align.globalms” function from the Biopython module pairwise2 was used with the parameter setting match = 2, mismatch = -1, gapOpen = -0.5 and gapExtend = -0.1. For our benchmark, we restricted the BLAST search to the phylum of the res […]
REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes
[…] m GenBank flatfiles through a semi-automated parsing algorithm implemented in custom python (2.7.13) scripts. Each flatfile is screened for RNA editing features using the SeqIO parser included in the Biopython (1.68) module (Cock et al., ).All annotations have been manually checked to identify and correct potential errors, taking into account other related flatfile fields or literature. REDIdb dat […]
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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).