Daniel Mapleson
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Additional file 11: of Correction to: Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta Open
HMM profiles used for Hmmsearch. (ZIP 1469 kb)
Efficient and accurate detection of splice junctions from RNA-seq with Portcullis Open
Next-generation sequencing technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression, and alternative splicing. Key to this is the accurate identificatio…
Leveraging multiple transcriptome assembly methods for improved gene structure annotation Open
We have implemented this method in an open-source Python3 and Cython program, Mikado, available on GitHub.
main_data_v2.tar.gz Open
Version 2 of the main set of junctions used within the paper. This version has been derived from more recent versions of the RNAseq aligners and Portcullis.
main_data.tar.gz Open
Junctions associated with the arabidopsis, drosophila and human datasets used in the Portcullis paper.
wheat.tar.gz Open
Splice junctions associated with our wheat experiments.
SPECTRE: a suite of phylogenetic tools for reticulate evolution Open
Summary Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and F…
Efficient and accurate detection of splice junctions from RNAseq with Portcullis Open
Next generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression and alternative splicing. Key to this is the the accurate iden…
Leveraging multiple transcriptome assembly methods for improved gene structure annotation Open
The performance of RNA-Seq aligners and assemblers varies greatly across different organisms and experiments, and often the optimal approach is not known beforehand. Here we show that the accuracy of transcript reconstruction can be booste…
SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution Open
Summary Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and F…
View article: Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom
Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom Open
Summary Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine p…
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species Open
Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. T…
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies Open
Motivation De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in …
KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies Open
Motivation De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a…
A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters Open
Background The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception, and the majority have evolved to colonise a small number of clos…