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.
Origin landscape of the Chagas disease parasite Trypanosoma cruzi
de Oliveira Vitarelli et al. from the Butantan Institute in Brazil used DNAscent to create a replication origin atlas of the T. cruzi genome. In doing so, they identified three classes of origins and showed how these origins may contribute to the rapid evolution of the genome's disruptive compartment.
Replication of the leishmaniasis parasite genomes
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.
First map of replication fork movement across ecDNA
We worked with Julian Sale's lab at the MRC LMB to show how replication forks move across extrachromosomal DNA. These circular chromosome fragments often harbour oncogenes that give cancer cells a selective advantage, and DNAscent showed that they are vulnerable to agents that disrupt DNA replication.
Fast, genome-wide maps of replication origins
We worked with Julian Sale's lab at the MRC LMB to develop ORILINX, a large language model that can detect the genomic location of replication origins, and showed that the model performs well across the human, chicken, sheep, and mouse genomes.
Fast, genome-wide maps of replication origins
Now, you can pass a FASTA file to ORILINX and you're only minutes away from a genome-wide origin map. ORILINX is freely available and open-source, just like all of our tools. It's new, so we're looking forward to working with it, and we're excited to see what you do with it too!
Detecting difficult-to-replicate regions of 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. Comparing the replication timing data to the model's predictions pinpointed regions where replication proceeds slower than would be expected.
A genome-wide model of replication fork movement in malaria parasites
DNAscent was able to create the first genome-wide map of replication fork movement in P. falciparum and the Beacon Calculus made it straightforward to fit a mathematical model to this data. Using the two approaches together in a systems biology approach allowed us to verify that our new map of fork movement agreed with expectation.
