UROPA is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature.
ASAP is designed to organize the data associated with a genome from the early stages of sequence annotation through genetic and biochemical characterization, providing a vehicle for ongoing updates of the annotation and a repository for genome-scale experimental data.
CRISPRdigger is a de novo CRISPR detection program which could identify more truncated DR and has higher accuracy and more contents in the test genomes compared with the present other tools-CRISPRFinder, CRT and PILER-CR.
MOAT is a computational system for identifying significant mutation burdens in genomic elements with an empirical, nonparametric method. Taking a set of variant calls and a set of annotations, MOAT calculates which annotations have observed variant counts that are substantially elevated with respect to a distribution of expected variant counts determined by permutation of the input data.
ALoFT provides extensive annotations to putative loss-of-function variants (LoF) in protein-coding genes including functional, evolutionary and network features. Further, ALoFT can predict the impact of premature stop variants and classify them as dominant disease-causing, recessive disease-causing and benign variants.
LARVA is a computational framework designed to facilitate the study of noncoding variants. It addresses issues that have made it difficult to derive an accurate model of the background mutation rates of noncoding elements in cancer genomes.