Want to analyze your BLAST results in the context of a genome browser? Want to compare those results against other genome assembly annotations? The BLAST widget, a new browser feature, lets you do that. It provides direct access within GDV to execute and manage BLAST queries (blastn, tblastn) aligned to the specific assembly displayed in GDV.
Several of the latest videos on the NCBI YouTube channel highlight NCBI resources. Subscribe to the channel to see all our new videos.
A brief introduction into how the BLAST widget, a new addition to the Genome Data Viewer, helps you see your BLAST results in the context of assembled genome sequences.
Highlights in release 109:
- A total of 20,203 protein-coding genes and 17,871 non-coding genes were annotated.
- The number of annotated curated transcripts increased by 17% and genes with two or more curated alternative variants increased by 8%.
- The annotation includes 6,862 features and 2,075 GeneIDs for non-genic functional elements, such as regulatory regions and known structural elements. For example, see the opsin locus control region (OPSIN-LCR).
On October 24, 2017, we announced the replacement of NCBI’s Map Viewer with the Genome Data Viewer (GDV) . As described in that announcement, the Map Viewer web interface will be removed in one week on May 2, 2018. Map Viewer links will be redirected to the GDV home page. Map Viewer static data will remain on the NCBI FTP site. Please review details related to the FTP content in our February announcement.
Please contact us with any comments and concerns, or if you need more help with the transition from Map Viewer to GDV.
We know it’s important to you to be able to browse and visually inspect variants and alignments from your next-gen sequencing experiments, so we’ve added remote streaming of BAM files to the Genome Data Viewer (GDV). All you need are your BAM files and the index files (.bai extension) in a location that allows HTTP access and you can stream BAM files as custom tracks into the GDV.
Several videos are up on the NCBI YouTube, including recordings of recent NCBI Minute webinars.
On Wednesday, November 1, 2017, we will present a webinar on GDV, NCBI’s full-featured genome browser. In this webinar, you’ll learn how to explore and analyze sequences and annotations for eukaryotic RefSeq genome assemblies. We’ll show you how to:
- Search across the entire assembly for genes, products and other markers or jump to a specific position or range
- Display any of seven preselected track sets highlighting various aspects of the assembly or create and load your own custom track sets from your NCBI account.
- Load and display submitted alignment data from NCBI’s GEO or SRA.
- Upload your own annotation and variant data
- Display BLAST or Primer-BLAST results on the assembly in the browser.
Date and time: Wednesday, November 1, 2017 12:00-12:30PM EDT
After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.
NCBI is pleased to announce the initial data release of RefSeq Functional Elements, a resource that provides RefSeq and Gene records for experimentally validated human and mouse non-genic functional elements. Data can be accessed via Gene, Nucleotide, BLAST, BioProject, Graphical Displays and FTP.