DeepSEA is a deep learning-based algorithmic framework for predicting the chromatin effects of sequence alterations with single nucleotide sensitivity. DeepSEA can accurately predict the epigenetic state of a sequence, including transcription factors binding, DNase I sensitivities and histone marks in multiple cell types, and further utilize this capability to predict the chromatin effects of sequence variants and prioritize regulatory variants.
ABrowse is an open source genome browser framework for not only end users, but also data providers and developers. Powered by cutting-edge technologies, ABrowse provides a rather comprehensive set of features as a modern next-generation genome browser framework
cis-Browser (cis-Regulatory Browser) is genome browser for cis-regulatory information inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation
BM-BC is a Bayesian method of base calling for Solexa-GA sequencing data. The Bayesian method builds on a hierarchical model that accounts for three sources of noise in the data, which are known to affect the accuracy of the base calls: fading, phasing, and cross-talk between channels.
VIRS is an interactive web-based program designed for restriction endonuclease cut sites prediction and visualisation. The system permits to simultaneously process batch DNA sequences, and produces visual restriction maps with several useful options for users’ customisation. These options also perform in-depth analysis of the restriction maps, such as virtual electrophoretic result for digested fragments. Different from other analytical tools, VIRS not only displays visual outputs, but also provides the detailed properties of enzymes that are commercially avaialbe. All the information correlates with enzymes is stored in our database, which is updated monthly from the manufacturers’ websites.
SToRM is a software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, or Illumina more classical encoding as well as the observed reading error distribution along the read.
BM-Map is a powerful NGS genomic loci mapping refiner. It improves the mapping of the multireads (reads mapped to more than one genomic location with similar fidelities), as a refinement step after the general read-alignment is completed.