Biopython statistics

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Protocols

Biopython specifications

Information


Unique identifier OMICS_04850
Name Biopython
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 1.71
Stability Stable
Requirements
matplotlib, Graphviz, NetworkX
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Biopython

Subtool


  • Bio.Phylo

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Eric Talevich
  • person_outline Biopython Team

Publications for Biopython

Biopython citations

 (313)
library_books

Profiling microbial strains in urban environments using metagenomic sequencing data

2018
Biol Direct
PMCID: 5944035
PMID: 29743119
DOI: 10.1186/s13062-018-0211-z

[…] 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 [ […]

library_books

OMGene: mutual improvement of gene models through optimisation of evolutionary conservation

2018
BMC Genomics
PMCID: 5923031
PMID: 29703150
DOI: 10.1186/s12864-018-4704-z

[…] 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. […]

call_split

Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice

2018
PLoS One
PMCID: 5919577
PMID: 29698444
DOI: 10.1371/journal.pone.0196434
call_split See protocol

[…] 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 […]

library_books

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain

2018
Antimicrob Agents Chemother
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] 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 […]

library_books

GLASSgo – Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence

2018
Front Genet
PMCID: 5913331
PMID: 29719549
DOI: 10.3389/fgene.2018.00124

[…] 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 […]

library_books

REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes

2018
Front Plant Sci
PMCID: 5904370
PMID: 29696033
DOI: 10.3389/fpls.2018.00482

[…] 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 […]

Citations

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Biopython institution(s)
Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain; James Hutton Institute, Invergowrie, UK; Harvard School of Public Health Bioinformatics Core, Boston, MA, USA
Biopython funding source(s)
Supported by Google Summer of Code 2009, the National Evolutionary Synthesis Center (NESCent) Phyloinformatics program and a FI-DGR from AGAUR.

Biopython review

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Zulko

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Desktop
Probably the most complete and generic library for Bioinformatics in Python, BioPython enjoys a broad user base, years of features contributions, and an extensive documentation.

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).