Our Tools
DNAscent​
Software that detects DNA base analogues in molecules sequenced on the Oxford Nanopore platform. We use this software to measure the movement and stalling of DNA replication forks across cancer genomes in response to therapeutic agents, but it can do a lot more than that and our team is hard at work on some exciting new features.
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Developers:
The new biology it's enabling:
How the leishmaniasis parasite Leishmania major replicates its genome
Damasceno et al. from the University of Glasgow used DNAscent to show that L. major replicates its genome using one highly efficient origin per chromosome together with a stochastic background of origins that localise to genomic regions of high AT-content and G-quadruplexes.
The Beacon Calculus
Our process algebra for modelling biological systems that makes simulating biological systems fast and easy. We maintain software that simulates these models so we can use it for all sorts of applications relating to genome stability.
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Developers:
The new biology it's enabling:
An algorithm to detect difficult-to-replicate regions across the human genome
We used the Beacon Calculus to create a model of human whole-genome replication that served as a "null hypothesis" of how replication should take place in the absence of stress. By comparing the replication timing data to the model's predictions, we can pinpoint regions where the two diverge indicating sites where replication proceeds slower than would be expected.