Announcing the NCBI SARS-CoV-2 Variant Calling Pipeline and Related Data Products

Still waiting for an analysis pipeline that can uniformly process raw sequence data produced by a variety of sequencing platforms? Your wait is over! Announcing the SARS-CoV-2 Variant Calling Pipeline, which is now operational and optimized to provide support for multiple sequencing platforms including, Illumina, Oxford Nanopore, and PacBio. This new pipeline can make allele … Continue reading Announcing the NCBI SARS-CoV-2 Variant Calling Pipeline and Related Data Products

NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer

Every so often, we gather our most recent videos in one post on the blog, for your convenience. Scroll down – and don’t forget to subscribe to our channel! Introducing GaPTools for dbGaP Submitters This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools … Continue reading NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer

Gene filtering in NCBI Sequence Viewer

We are excited to announce new track display options for gene annotation tracks in the NCBI Genome Data Viewer genome browser and other instances of the NCBI Sequence Viewer! Now, you can simplify gene annotation tracks to show only the genes and transcripts that you care about most.  For instance, you can choose to hide … Continue reading Gene filtering in NCBI Sequence Viewer

June 2 Webinar: Quickly upload and view your own data in genomic context at NCBI

Join us on June 2, 2021 at 12PM eastern time to learn how to how to upload and display your own genomic data in the context of annotated genome assemblies. You will use the Genome Data Viewer and the Sequence viewer to visualize your own uploaded data (indexed BAM, VCF, BED, wig, GFF formats), data … Continue reading June 2 Webinar: Quickly upload and view your own data in genomic context at NCBI

View intron feature evidence in the Genome Data Viewer and Sequence Viewer

Are you a researcher who works on gene biology and are interested in alternative splice patterns in your gene or genes of interest?  If so, be sure to explore the intron feature evidence available in graphics views of genome assemblies annotated by NCBI. You can view the NCBI evidence used for calling splice variant for … Continue reading View intron feature evidence in the Genome Data Viewer and Sequence Viewer

Primer-BLAST now designs primers for a group of related sequences

Primer-BLAST now has a “Primers common for a group of sequences” submission tab that allows you to design primers for a group of highly similar sequences. For example, you may want test for expression of any transcript of gene rather than a specific splice variant, so you want to design primers to cover all transcript … Continue reading Primer-BLAST now designs primers for a group of related sequences

Improved chromosome searching in Genome Browsers

Are you interested in searching for a chromosomal region in a genome, but don’t know how to write the correct query?  The good news is that the NCBI Genome Data Viewer (GDV) now supports a much wider array of search options. Some examples are listed below: chr1:1,500,000-2,000,000 chr2: 1.5M – 2M chr2: 1.5M-2,540.2K 2:1,500,000-2,000,000 3: … Continue reading Improved chromosome searching in Genome Browsers

Coronavirus host gene regulatory elements now annotated by RefSeq Functional Elements

The COVID-19 pandemic has drawn attention to the human host genes associated with SARS-CoV-2 entry and to the elements that regulate expression of these genes. At NCBI, we have prioritized curation of experimentally validated regulatory elements for these genes in the RefSeq Functional Elements project. Our annotations include several enhancers, promoters, cis-regulatory elements and protein binding … Continue reading Coronavirus host gene regulatory elements now annotated by RefSeq Functional Elements

Try out our new table download options from the NCBI genome browsers and sequence viewers!

Have you ever wanted a list of the genes you’re looking at in the browser – maybe to give you a starting point for candidate gene analysis, or to cross-reference with other data? In response to your feedback and helpful … Continue reading

Vector graphics downloads now available in NCBI genome browsers and sequence views

You can now download images in both PDF and Scaled Vector Graphics (SVG) formats from our Sequence Viewer and genome browsers such as the Genome Data Viewer!  SVG files are ideal for editing in image editors and provide high quality … Continue reading