Tag: Sequence Viewer

Tour the NCBI’s Genome Data Viewer, Bookshelf, Pathogen Isolates Detection Browser and other resources on YouTube

Several of the latest videos on the NCBI YouTube channel highlight NCBI resources. Subscribe to the channel to see all our new videos.

NCBI’s Genome Data Viewer – Introducing the BLAST Widget

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.

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Human annotation release 109 for GRCh38.p12 is available in RefSeq

Human annotation release 109 for GRCh38.p12 is available in RefSeq

You can now download human annotation release 109 on FTP or explore it in the Genome Data Viewer, in the Gene database, and with BLAST.

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).

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NCBI retires Map Viewer web interface

NCBI retires Map Viewer web interface

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.

Sequence Viewer 3.25 now available

Sequence Viewer 3.25 now available

Sequence Viewer 3.25 has several new features, improvements and bug fixes, including a new user interface and programmatic API to attach and show HTTP based BAM files, as well as improved usability of zoom functions and tooltips for RNA features. For a full list of changes, see the Sequence Viewer release notes.

Sequence Viewer is a graphical view of sequences and color-coded annotations on regions of sequences stored in the Nucleotide and Protein databases.

See your data in context with NCBI’s updated Genome Data Viewer

See your data in context with NCBI’s updated Genome Data Viewer

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.

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Map Viewer retirement: New FTP directory paths

Map Viewer retirement: New FTP directory paths

In October of last year, we announced the replacement of NCBI’s Map viewer with the Genome Data Viewer (GDV).  Here are some additional details on how to access to the older Map Viewer FTP content going forward and some information to help you with the transition to GDV.

As we announced last fall, we are no longer updating the data content of Map Viewer FTP directories. To help avoid any confusion over the meaning of the directory names,  we will alter the CURRENT and PREVIOUS directories under the species directories in the Map Viewer FTP area so that they no longer point to data. However, the existing data will still be available on the FTP site.

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5 NCBI articles in 2018 Nucleic Acids Research database issue

5 NCBI articles in 2018 Nucleic Acids Research database issue

The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

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November 1 webinar: Introducing the Genome Data Viewer (GDV)

November 1 webinar: Introducing the Genome Data Viewer (GDV)

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’s Genome Data Viewer (GDV) to replace Map Viewer

The Genome Data Viewer (GDV) is now the main genome browser at NCBI replacing the Map Viewer, our original genome browser. GDV is a modern genome browser with essential improvements over Map Viewer. These include sequence-level details and an automated update process that keeps up with the rapid pace of genome sequencing, assembly and annotation.

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The Genome Data Viewer homepage (top panel) and browser view (bottom panel)

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