Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools
As part of our ongoing effort to enhance your experience, we are updating the NCBI Datasets application programming interfaces (APIs). Beginning in June 2024, the v2alpha APIs will be promoted to the stable v2 version. At this time, the v1 API, the command-line interface (CLI) version 13 and older versions, and the Python library v1 … Continue reading Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools → (Source: NCBI Insights)
Source: NCBI Insights - February 20, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New API NCBI Datasets Source Type: news
NCBI Celebrates International Love Data Week
Providing free and open access to scientific literature and data Do you love biological data? Join NCBI in celebrating International Love Data Week, February 12-16, 2024! Love Data Week is an international celebration of data, which takes place every year during the week of Valentine’s Day. This year’s theme is “My Kind of Data,” focusing on … Continue reading NCBI Celebrates International Love Data Week → (Source: NCBI Insights)
Source: NCBI Insights - February 12, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Biomedical data Source Type: news
New RefSeq Annotations Now Available!
During October to January, the NCBI Eukaryotic Genome Annotation Pipeline released seventy new annotations in RefSeq! New Annotations Alnus glutinosa (eudicot) Amyelois transitella (moth) Anolis sagrei ordinatus (Brown anole) Apis cerana (Asiatic honeybee) Balaenoptera ricei (Rice’s whale) Bombus pascuorum (bee) Bos javanicus (banteng) Bos taurus (cattle) Cannabis sativa (eudicot) Colius striatus (speckled mousebird) Cololabis saira (Pacific saury) … Continue reading New RefSeq Annotations Now Available! → (Source: NCBI Insights)
Source: NCBI Insights - February 7, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) Eukaryote Genome Annotation Pipeline (EGAP) Genome Data Viewer (GDV) NCBI Datasets RefSeq Source Type: news
Enhancements to ClinVar Website Now Live
As previously announced, we updated the ClinVar website as part of our effort to better support the display of submitted somatic variation data. What changed? Updated ClinVar search results Germline / Somatic origin filter Somatic Classification and Review Status summary Updated Variant (VCV) record page Includes both Germline and Somatic data for the same variant … Continue reading Enhancements to ClinVar Website Now Live → (Source: NCBI Insights)
Source: NCBI Insights - January 31, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New ClinVar Source Type: news
HomoloGene Now Redirects to NCBI Datasets Gene
A new way to view and download related genes As previously announced, HomoloGene now automatically redirects to the NCBI Datasets Gene page giving you easy access to up-to-date sequence and homology data. The NCBI Datasets Gene Table provides a link to NCBI Orthologs with expanded gene and protein information and links to tools. NCBI Orthologs … Continue reading HomoloGene Now Redirects to NCBI Datasets Gene → (Source: NCBI Insights)
Source: NCBI Insights - January 30, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) Gene Homologs NCBI Datasets Source Type: news
BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024
Easily generate BLAST FASTA files yourself! In April 2024, the FASTA (sequence text) files of the sequences in the Basic Alignment Search Tool (BLAST) databases will no longer be available on the FTP site. However, you can easily generate FASTA files yourself from the formatted BLAST databases by using the BLAST utility blastdbcmd that comes … Continue reading BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024 → (Source: NCBI Insights)
Source: NCBI Insights - January 25, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) FASTA NCBI Taxonomy Source Type: news
Updated Bacterial and Archaeal Reference Genome Collection is Available!
Download the updated bacterial and archaeal reference genome collection! This collection (18,941 genomes as of Jan 18, 2024) was built by selecting the “best” genome assembly for each species among the 330,000+ prokaryotic genomes in RefSeq (except for E. coli for which two assemblies were selected as reference). You can speed up your sequence searches … Continue reading Updated Bacterial and Archaeal Reference Genome Collection is Available! → (Source: NCBI Insights)
Source: NCBI Insights - January 18, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) NCBI Taxonomy Nucleotide BLAST (blastn) Prokaryotic genome annotation RefSeq Source Type: news
RefSeq Release 222 Now Available!
Check out RefSeq release 222, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets. What’s included in this release? As of January 8, 2024, this full release incorporates genomic, transcript, and protein data containing: 411,137,832 records 304,562,770 proteins 59,343,570 RNAs sequences from 145,371 organisms The release is provided in several directories as … Continue reading RefSeq Release 222 Now Available! → (Source: NCBI Insights)
Source: NCBI Insights - January 16, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Comparative Genomics Resource (CGR) NCBI Datasets RefSeq Source Type: news
Now Available: NCBI Hidden Markov Models (HMM) Release 14.0!
Download release 14.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP)! Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. What’s new? Release 14.0 contains: 16,383 HMMs maintained by NCBI 252 new HMMs since release 13.0 Several … Continue reading Now Available: NCBI Hidden Markov Models (HMM) Release 14.0! → (Source: NCBI Insights)
Source: NCBI Insights - January 11, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Hidden Markov Models (HMM) HMMER NCBI Prokaryotic Genome Annotation Pipeline (PGAP) RefSeq Source Type: news
Best of 2023: A Look at the NCBI Insights Blog
As we begin a new year, let’s look back at the best NCBI Insights Blog posts of 2023. In case you missed any of these, check them out! Learn more The NCBI Insights Blog is intended to help you better understand NCBI and our resources, explore issues of scientific interest that drive our resource development, … Continue reading Best of 2023: A Look at the NCBI Insights Blog → (Source: NCBI Insights)
Source: NCBI Insights - January 4, 2024 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news
GenBank Release 259.0 is Available!
GenBank release 259.0 (12/22/2023) is now available on the NCBI FTP site. This release has 27.94 trillion bases and 3.96 billion records. The current release has: 247,777,761 traditional records containing 2,433,391,164,875 base pairs of sequence data 2,775,205,599 WGS records containing 23,600,199,887,231 base pairs of sequence data 701,336,089 bulk-oriented TSA records containing 659,924,904,311 base pairs of … Continue reading GenBank Release 259.0 is Available! → (Source: NCBI Insights)
Source: NCBI Insights - December 28, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news
Using NCBI Data and Tools for Your Research Project
Are you a biology student working on a research project? NCBI offers free access to a wide variety of resources and tools to help you find and download data for your project. How and why do you use our resources? Check out the example below: Your professor has assigned you a research project looking at … Continue reading Using NCBI Data and Tools for Your Research Project → (Source: NCBI Insights)
Source: NCBI Insights - December 18, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Comparative Genome Viewer (CGV) Gene Genome Data Viewer (GDV) iCn3D NCBI Datasets NCBI Taxonomy PubMed Central (PMC) Source Type: news
Update to GenBank Qualifier
‘Country’ will transition to ‘Geographic Location’ effective June 2024 As announced earlier this year, we will begin to systematically gather ‘location of collection’ and ‘date and time of collection’ for sequence data submitted to GenBank and the Sequence Read Archive (SRA). As part of this effort and to make location data more accurate and informative, we are also changing the … Continue reading Update to GenBank Qualifier → (Source: NCBI Insights)
Source: NCBI Insights - December 14, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Sequence Read Archive (SRA) Source Type: news
View Global Distribution of Microbial AMR Genes with the New MicroBIGG-E Map
Graphical display provides new way to explore data! NCBI’s Pathogen Detection project provides the Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E) which lets you browse anti-microbial resistance (AMR), stress response, virulence genes, and genomic elements found in genomes from the NCBI Isolates Browser. We are excited to introduce the MicroBIGG-E Map, an … Continue reading View Global Distribution of Microbial AMR Genes with the New MicroBIGG-E Map → (Source: NCBI Insights)
Source: NCBI Insights - December 6, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Antimicrobial resistance NCBI Pathogen Detection Source Type: news
Coming Soon! Updates to the ClinVar Website
In order to support the inclusion of submitted somatic variation data, we are updating the ClinVar website. In early 2024, you will begin to see some changes. What will change? Variant (VCV) record pages will have an updated look and feel: Simpler layout with no tabs New sections will display somatic classifications Summary section will … Continue reading Coming Soon! Updates to the ClinVar Website → (Source: NCBI Insights)
Source: NCBI Insights - November 28, 2023 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New ClinVar Source Type: news
