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Identification of regulatory DNA elements and non-coding genetic variants that underlie traits and diseases in humans, plants and animals. Assay the functional impact of non-coding mutations for entire genomes or specific mutation panels. The SuRE method is in essence a strategy to analyze millions of DNA elements for their activity as promoters or enhancers in a single experiment.

The only required input is DNA and once a SuRE library is established it can be analyzed and compared to other DNA sources in the controlled environment of any transfectable cell type. Thus, without the requirement of invasive biopsies, any genome of interest can be analyzed in relevant cell types and under relevant e. We first construct a plasmid library containing millions of DNA elements. A human genome is randomly sheared, size-selected and cloned into a plasmid library that contains no promoter of its own.

These plasmids contain a unique 20bp sequence referred to as a barcode which allows us to uniquely identify and follow each cloned DNA element. This library is characterized i. Fragmented human genome. In step 2, the plasmid library is transfected into a cell type of interest.

DNA elements containing promoters or enhancers will transcribe the barcode which can now be detected in the RNA by high-throughput sequencing. By comparing these barcode frequencies with the frequencies in the plasmid library, a quantitative map of promoter and enhancer activity can be constructed for the human genome. The database files include gzipped genome annotation for each chromosome. After comparison, annogen will generate html report about the features in two conditions.

Energy, entropy, GC content and homology score figures are displayed side by side for comparison. Skip to content. Star 1. MIT License. Branches Tags. Could not load branches. Could not load tags. Latest commit. BMC Bioinformatics. Yara is an exact tool for aligning DNA sequencing reads to reference genomes.

It works by spliting a given reference database in to smaller manageble partitions and this allows faster indexing and super fast updating time.

Temesgen Hailemariam Dadi. NAR Genom Bioinform. MetaMeta is a pipeline to execute and integrate results from metagenome analysis tools. It provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. Vitor C. MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling. DUDes is a reference-based taxonomic profiler with a top-down approach to analyze metagenomic NGS samples.

DUDes: a top-down taxonomic profiler for metagenomics.