Tools, Libraries & Scripts

Biopython

The programming expertise within ICS spans many programming languages, but on the bioinformatics side our local Pythonistas are also regular contributors to the open source library Biopython, described in Cock et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics.

GenomeDiagram

Written in Python and originally released as a separate library, GenomeDiagram is now part of the larger Biopython project. See Pritchard et al. (2006) GenomeDiagram: a python package for the visualization of large-scale genomic data.

find_differential_primers

The find_differential_primers script is a tool to aid finding discriminatory PCR primers among genomes or other biological sequences of interest. It has been used to design discriminatory primers specific to outbreak E.coli O104:H4 strains, to individual species of Dickeya plant pathogenic bacteria, and to discriminate between oomycete effector proteins, for population studies.

See Pritchard et al. (2012) Alignment-free design of highly discriminatory diagnostic primer sets for Escherichia coli O104:H4 outbreak strains, and Pritchard et al. (2013) Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences.

pyADHoRe

pyADHoRe is a module that provides a basic data object and parser for manipulating and processing output of the i-ADHoRe 3.0 bioinformatics tool into Python.