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).
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.
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.
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.
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.
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
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.