Biopython protocols

View Biopython computational protocol

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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

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Documentation


Maintainers


  • person_outline Eric Talevich <>
  • person_outline Biopython Team <>

Publications for Biopython

Biopython in pipelines

 (26)
2018
PMCID: 5822837
PMID: 29479501
DOI: 10.7717/peerj.4402

[…] circular genome map was assembled from p. glacincola bnf20 genbank formatted file (nz_liqb00000000.1) using the plotmygbk wrapper script (https://github.com/microgenomics/plotmygbk); plotmygbk uses biopython and the r platform with the packages rsamtools, omiccircos, and data.table to produce a vector image of a circular map (; ; ; ; https://github.com/rdatatable/data.table)., raw sequence data […]

2018
PMCID: 5838928
PMID: 29527141
DOI: 10.1186/s12014-018-9188-y

[…] proteins was performed with panther (v11.1) [, ]. the open, web-based platform galaxy [, ] was used to calculate the identified proteins’ molecular weight, isoelectric point and gravy score with biopython [] as well as potential transmembrane domains with a hidden markov model [, ]. in case of peptides containing selenocysteine the single amino acid “u” was deleted in order to obtain a gravy […]

2018
PMCID: 5919577
PMID: 29698444
DOI: 10.1371/journal.pone.0196434

[…] 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 […]

2018
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] toolkit v3.2.2 []. coding sequence alignments of reference and snv-containing genomes were generated for gene regions of 14 × or greater sequencing coverage using customised python scripts and biopython []. coding dna sequences (cds) were excluded where sequencing coverage at > 14 × made up less than 50% of the cds. dn/ds ratios and synonymous/non-synonymous mutations were calculated […]

2018
PMCID: 5923442
PMID: 29587397
DOI: 10.3390/v10040148

[…] 420–474) that the vaccine construct targets. within each selected uid family (figure 3b), we aligned reads using mafft (a multiple sequence alignment program) and built a consensus sequence using biopython (gap_consensus). geneious and bioedit were used to convert the nucleotide sequences into amino acid sequences and to study mutations. the shannon diversity index was calculated [] […]


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Biopython in publications

 (402)
PMCID: 5944035
PMID: 29743119
DOI: 10.1186/s13062-018-0211-z

[…] 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 […]

PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] toolkit v3.2.2 []. coding sequence alignments of reference and snv-containing genomes were generated for gene regions of 14 × or greater sequencing coverage using customised python scripts and biopython []. coding dna sequences (cds) were excluded where sequencing coverage at > 14 × made up less than 50% of the cds. dn/ds ratios and synonymous/non-synonymous mutations were calculated […]

PMCID: 5919577
PMID: 29698444
DOI: 10.1371/journal.pone.0196434

[…] 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 […]

PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] 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 […]

PMCID: 5916898
PMID: 29695722
DOI: 10.1038/s41467-018-04084-0

[…] content of the different motifs, we calculated the normalized motif score, defined here as the maximum motif score for the oligo sequence used divided by the patser motif significance threshold in biopython., we compared publically available chip-seq data for swi/snf, prc2, and nurd subunits, with publically available g4-sequencing data (supplementary table ). all sequencing datasets […]


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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).