Influenza sequence validation and annotation using VADR.

Tens of thousands of influenza sequences are deposited into the GenBank database each year. The software tool FLu ANnotation tool (FLAN) has been used by GenBank since 2007 to validate and annotate incoming influenza sequence submissions and has been publicly available as a webserver but not as a standalone tool. Viral Annotation DefineR (VADR) is a general sequence validation and annotation software package used by GenBank for norovirus, dengue virus and SARS-CoV-2 virus sequence processing that is available as a standalone tool.

Influenza sequence validation and annotation using VADR.

Tens of thousands of influenza sequences are deposited into the GenBank database each year. The software tool FLAN has been used by GenBank since 2007 to validate and annotate incoming influenza sequence submissions, and has been publicly available as a webserver but not as a standalone tool. VADR is a general sequence validation and annotation software package used by GenBank for Norovirus, Dengue virus and SARS-CoV-2 virus sequence processing that is available as a standalone tool.

Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank.

Rapid response to the current coronavirus disease 2019 (COVID-19) pandemic requires fast dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequence data in order to align diagnostic tests and vaccines with the natural evolution of the virus as it spreads through the world. To facilitate this, the National Library of Medicine's National Center for Biotechnology Information developed an automated pipeline for the deposition and quick processing of SARS-CoV-2 genome assemblies into GenBank for the user community. The pipeline ensures the collection of contextual information about the virus source, assesses sequence quality and annotates descriptive biological features, such as protein-coding regions and mature peptides.

Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex.

Long-range enhancer-promoter interactions are commonly seen in complex genetic loci such as Hox genes and globin genes. In the case of the Drosophila Antennapedia complex, the T1 enhancer bypasses the neighboring ftz gene and interacts with the distant Scr promoter to activate expression in posterior head segments. Previous studies identified a 450-bp promoter-proximal sequence, the tethering element, which is essential for T1-Scr interactions.

Coordinate regulation of an extended chromosome domain.

Spitz et al (2003[this issue of Cell]) describe the properties of a novel cis-regulatory DNA element, the global control region (GCR), which regulates gene expression over distances of several hundred kilobases at the mouse HoxD complex. The GCR provides an explanation for the colinear genetic linkage and expression of individual Hox genes within developing limbs.

Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex.

The correct spatial expression of two Drosophila bithorax complex (BX-C) genes, abdominal-A (abdA) and Abdominal-B (AbdB), is dependent on the 100-kb intergenic infraabdominal (iab) region. The iab region is known to contain a number of different domains (iab2 through iab8) that harbor cis-regulatory elements responsible for directing expression of abdA and AbdB in the second through eighth abdominal segments. Here, we use in situ hybridization to perform high-resolution mapping of the transcriptional activity in the iab control regions.

Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex.

Insulator DNAs and promoter competition regulate enhancer-promoter interactions within complex genetic loci. Here we provide evidence for a third mechanism: promoter-proximal tethering elements. The Scr-ftz region of the Antennapedia gene complex includes two known enhancers, AE1 and T1.