Important Update About How You Log Into your NCBI Accounts
As mentioned in a previous blog post, we are transitioning to using 3rd party logins for all My NCBI accounts. We are doing this because NIH, NLM, and NCBI take your privacy and security very seriously. Transitioning to 3rd parties who have modern and industry-standard security practices ensures that you have the highest level of … Continue reading Important Update About How You Log Into your NCBI Accounts → (Source: NCBI Insights)
Source: NCBI Insights - February 26, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New My Bibliography My NCBI SciENcv Source Type: news

NIH ’s Sequence Read Archive to be made available on AWS’s Open Data Sponsorship Program
National Library of Medicine’s (NLM) National Center for Biotechnology Information (NCBI) and Amazon Web Services (AWS) are happy to announce that the controlled- and public-access Sequence Read Archive (SRA)–one of the world’s largest repositories of raw next generation sequencing data–will be freely accessible from Amazon S3 via the Open Data Sponsorship Program (ODP) as of … Continue reading NIH’s Sequence Read Archive to be made available on AWS’s Open Data Sponsorship Program → (Source: NCBI Insights)
Source: NCBI Insights - February 25, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New and Sustainability (STRIDES) Cloud computing NIH Science and Technology Research Infrastructure for Discovery Open data Sequence Read Archive (SRA) Source Type: news

The Datasets command-line tool now provides ortholog data
You can now get gene ortholog data using the NCBI Datasets command-line tool using a gene ID, gene symbol, or RefSeq nucleotide or protein accession. Data are available for vertebrates and insects. The vertebrate orthologs includes a specialized set for fish.  (See our recent post for more information on the orthologs for fish and insects.) You … Continue reading The Datasets command-line tool now provides ortholog data → (Source: NCBI Insights)
Source: NCBI Insights - February 23, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets Downloading data Gene Homologs RefSeq Source Type: news

Improvements to NCBI Assembly
NCBI’s genome Assembly has a number of significant improvements! Assembly records now have a link to Primer-BLAST making it easy to design primers in the context of a specific eukaryote genome assembly.  Figure 1 shows the Assembly page for the Genome Reference Consortium Mouse Build 39 (GRCm39) with the link to Primer-BLAST. Figure 1. The … Continue reading Improvements to NCBI Assembly → (Source: NCBI Insights)
Source: NCBI Insights - February 18, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly Eukaryotic genome annotation NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Primer-BLAST Source Type: news

New release of the Read Assembly and Annotation Pipeline Tool (RAPT), now 2X faster!
There is a new release of the Read assembly and Annotation Pipeline Tool (RAPT) available from our GitHub site. RAPT is a one-step application for the genome assembly and gene annotation of archaeal and bacterial isolates that can run on your local computer or the Google Cloud Platform (GCP). With this new release, jobs will … Continue reading New release of the Read Assembly and Annotation Pipeline Tool (RAPT), now 2X faster! → (Source: NCBI Insights)
Source: NCBI Insights - February 12, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Genome annotation Genome assemblies NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Read assembly and Annotation Pipeline Tool (RAPT) Source Type: news

Announcing the RefSeq annotation of rat mRatBN7.2!
NCBI RefSeq has finished its initial annotation of the new rat reference assembly, mRatBN7.2, recently released by the Darwin Tree of Life Project at the Wellcome Sanger Institute. This is the first coordinate-changing update to the rat reference since the 2014 release of Rnor_6.0 from the Rat Genome Sequencing Consortium and brings the rat assembly into … Continue reading Announcing the RefSeq annotation of rat mRatBN7.2! → (Source: NCBI Insights)
Source: NCBI Insights - February 12, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets Gene Genome annotation Genome Data Viewer (GDV) NCBI Genome Remapping Service (NCBI Remap) Reference genome RefSeq Source Type: news

March 3 Webinar: Changes are coming to the way you log in to your NCBI account
Join us on March 3, 2021 to learn about changes to NCBI account log ins that will affect those of you who sign in directly your NCBI account.  After June 1, 2021 you will need to log in using your institution, social media, Google, Microsoft or login.gov account username and password. In this webinar, you … Continue reading March 3 Webinar: Changes are coming to the way you log in to your NCBI account → (Source: NCBI Insights)
Source: NCBI Insights - February 9, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New My Bibliography My NCBI Submissions Source Type: news

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 → (Source: NCBI Insights)
Source: NCBI Insights - February 2, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation Genome assemblies Genome Browser Genome Data Viewer (GDV) RNA-Seq Sequence Viewer Source Type: news

October-December eukaryotic genome annotations in Refseq
Since October, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for a large number of organisms. We’ve separated them by group; click on “details” to see the full list for each. Mammals Artibeus jamaicensis (Jamaican fruit-eating bat) Arvicola amphibius (Eurasian water vole) Balaenoptera musculus (Blue whale) Cebus imitator (Panamanian white-faced capuchin) Chlorocebus sabaeus … Continue reading October-December eukaryotic genome annotations in Refseq → (Source: NCBI Insights)
Source: NCBI Insights - January 28, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation RefSeq Source Type: news

Introducing MicroBIGG-E, a browser for microbial AMR genes and other stress and resistance elements
The Pathogen Detection project now offers the Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E) that lets you browse anti-microbial resistance (AMR), stress response,  virulence genes and genomic elements found in GenBank published isolate genomes from the NCBI Isolates Browser.  Unlike the  Isolates Browser that provides only a strain-level view of both published … Continue reading Introducing MicroBIGG-E, a browser for microbial AMR genes and other stress and resistance elements → (Source: NCBI Insights)
Source: NCBI Insights - January 25, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

Allele Frequency Aggregator (ALFA) Release 2 is available!
We are excited to announce the NCBI Allele Frequency Aggregator (ALFA) Release 2 (version 20201027095038) as one of the largest and most comprehensive aggregated variant datasets with allele frequency available as open-access. This release contains 79 dbGaP studies that included 192 thousand subjects and 5.8 trillion combined genotypes that generated allele frequency for 904 million … Continue reading Allele Frequency Aggregator (ALFA) Release 2 is available! → (Source: NCBI Insights)
Source: NCBI Insights - January 22, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New dbGaP Allele Frequency Aggregator (ALFA) Source Type: news

NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets
It’s time we do another roundup of what’s been happening on YouTube! First up, the NCBI YouTube channel has merged with the NLM YouTube channel. You’ll now be able to find diverse content all on one channel, from tips on using resources to fascinating moments in the history of medicine and more! Use RAPT, the … Continue reading NCBI on YouTube: RAPT and BLAST+ on the Cloud, SARS-CoV-2 genome data in Datasets → (Source: NCBI Insights)
Source: NCBI Insights - January 15, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: Quick Tips BLAST Datasets National Library of Medicine (NLM) Read assembly and Annotation Pipeline Tool (RAPT) SARS-CoV-2 Source Type: news

RefSeq release 204 is now available
online, from the FTP site and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of January 4, 2021, and contains 262,714,372 records, including 191,411,721 proteins, 35,353,412 RNAs, and sequences from 106,581 organisms. The release is provided in several directories as a complete dataset … Continue reading RefSeq release 204 is now available → (Source: NCBI Insights)
Source: NCBI Insights - January 14, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation Human genome RefSeq Source Type: news

Prokaryotic representative genomes updated — now over 13 thousand assemblies!
We have updated the bacterial and archaeal representative genome collection!  The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 11% since August 2020.  We’ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and … Continue reading Prokaryotic representative genomes updated — now over 13 thousand assemblies! → (Source: NCBI Insights)
Source: NCBI Insights - January 12, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly NCBI Nucleotide Prokaryotic genome annotation Protein Representative genome Source Type: news

GenBank release 241.0
(12/21/2020) is now available on the NCBI FTP site. This release has 12.98 trillion bases and 2.27 billion records. The current release has 221,467,827 traditional records containing 723,003,822,007 base pairs of sequence data. There are also 1,517,995,689 WGS records containing 11,830,842,428,018 base pairs of sequence data, 446,397,378 bulk-oriented TSA records containing 392,206,975,386 … Continue reading GenBank release 241.0 → (Source: NCBI Insights)
Source: NCBI Insights - January 7, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news

Retrieve genome data by BioProject using the Datasets command-line tool
You can now retrieve genome data using the NCBI Datasets command-line tool and API by simply providing a BioProject accession.  You can go directly from a BioProject accession to genome data even when the BioProject accession is the parent of multiple BioProjects (Figure 1). Figure 1. Command-lines using BioProject accessions with the datasets command-line tool and sample metadata. Top … Continue reading Retrieve genome data by BioProject using the Datasets command-line tool → (Source: NCBI Insights)
Source: NCBI Insights - January 5, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New BioProject Datasets Genome Metadata Source Type: news

Important Changes to NCBI Accounts Coming in 2021
Do you login to NCBI to use MyNCBI, SciENcv, or MyBibliography? Do you submit data to NCBI? If so, you’ll want to read further to get a first glimpse at some important changes to NCBI accounts that will be coming in 2021. What’s happening? In brief, NCBI will be transitioning to federated account credentials. NCBI-managed … Continue reading Important Changes to NCBI Accounts Coming in 2021 → (Source: NCBI Insights)
Source: NCBI Insights - January 5, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New My Bibliography My NCBI SciENcv Source Type: news

Expanding access to coronavirus-related literature: the COVID-19 Initiative in PMC reaches 100K articles!
One important way the National Library of Medicine (NLM) is responding to the ongoing public health emergency is through the COVID-19 Initiative. This public-private cooperation between NLM and more than 50 scholarly publishers and societies allows you to access over 100,000 articles on COVID-19, SARS-CoV-2 and other coronaviruses through PubMed Central (PMC). This collection includes … Continue reading Expanding access to coronavirus-related literature: the COVID-19 Initiative in PMC reaches 100K articles! → (Source: NCBI Insights)
Source: NCBI Insights - December 21, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New coronavirus PubMed Central (PMC) Source Type: news

NCBI hidden Markov models (HMM) release 4.0 now available!
Release 4.0 of the NCBI hidden Markov models (HMM) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available from our FTP site. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. This release contains 17,443 models, including 94 new models since the … Continue reading NCBI hidden Markov models (HMM) release 4.0 now available! → (Source: NCBI Insights)
Source: NCBI Insights - December 21, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Hidden Markov Models (HMM) HMMER PGAP Protein Family Model RefSeq Source Type: news

The Protein Family Model resource is now available!
The new Protein Family Model resource  (Figure 1) provides a way for you to search across the evidence used by the NCBI annotation pipelines to name and classify proteins. You can find protein families by gene symbol, protein function, and many other terms. You have access to related proteins in the family and publications describing … Continue reading The Protein Family Model resource is now available! → (Source: NCBI Insights)
Source: NCBI Insights - December 18, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New BLAST Conserved Domains Database (CDD) Hidden Markov Models (HMM) HMMER PGAP Protein Protein Family Model RefSeq SPARCLE Source Type: news

NCBI Virus: Test drive our new SARS-CoV-2 interactive data dashboard!
Are you looking for SARS-CoV-2 sequence data? Look no further! The NCBI Virus SARS-CoV-2 Data Hub now has an interactive data dashboard (Figure 1) that shows the collection location (country and US state), the date of collection, and the date of public availability for SARS-CoV-2 sequence data. You can view available nucleotide and protein sequences based … Continue reading NCBI Virus: Test drive our new SARS-CoV-2 interactive data dashboard! → (Source: NCBI Insights)
Source: NCBI Insights - December 3, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

December 9 Webinar: Using BLAST+ in Docker and on the cloud
Join us on December 9, 2020 to learn about containerized BLAST+ in Docker that is ready to use locally and in the cloud. We are staging BLAST databases in some cloud providers making running containerized BLAST as part of a pipeline in the cloud even easier. In this webinar you will learn about the advantages … Continue reading December 9 Webinar: Using BLAST+ in Docker and on the cloud → (Source: NCBI Insights)
Source: NCBI Insights - November 30, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New BLAST cloud computing webinars Source Type: news

Read assembly and Annotation Pipeline Tool (RAPT) is available for use and testing
We are excited to launch a beta version of RAPT, the Read assembly and Annotation Pipeline Tool, a one-step application for the genome assembly and gene annotation of archaeal and bacterial isolates. Start from an Illumina run in SRA or on your local machine and get a fully annotated genome! A RAPT Docker container includes … Continue reading Read assembly and Annotation Pipeline Tool (RAPT) is available for use and testing → (Source: NCBI Insights)
Source: NCBI Insights - November 24, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New RAPT Source Type: news

New Columns added to the web BLAST Descriptions Table
In response to your requests, we have added new columns to the Descriptions Table for the web BLAST output. The new columns are  Scientific Name, Common Name, Taxid, and Accession Length. Common Name and Accession Length are now part of the default display. You can click ‘Select columns’ or ‘Manage columns’ to add or remove … Continue reading New Columns added to the web BLAST Descriptions Table → (Source: NCBI Insights)
Source: NCBI Insights - November 23, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

Customize columns in NCBI ’s Multiple Sequence Alignment Viewer
We’re excited to report that researchers using the NCBI Multiple Sequence Alignment Viewer (MSAV) can now add or remove columns from the alignment view. In this way, you can choose to show only columns with data relevant for analysis of the sequences in your alignment. When you arrive at an MSA alignment view, you’ll see … Continue reading Customize columns in NCBI’s Multiple Sequence Alignment Viewer → (Source: NCBI Insights)
Source: NCBI Insights - November 20, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Multiple Sequence Alignment Viewer Source Type: news

December 2 Webinar: Using the new Read assembly and Annotation Pipeline Tool (RAPT) to assemble and annotate microbial genomes
Join us December 2 to learn how to use the Read assembly and Annotation Pipeline Tool (RAPT). With RAPT, you can assemble and annotate a microbial genome right out of the sequencing machine! Provide the short genomic reads or an SRA run on input, and get back the sequence annotated with coding and protein coding … Continue reading December 2 Webinar: Using the new Read assembly and Annotation Pipeline Tool (RAPT) to assemble and annotate microbial genomes → (Source: NCBI Insights)
Source: NCBI Insights - November 20, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New cloud computing genome annotation genome assemblies Next-gen sequencing RAPT webinars Source Type: news

Search NCBI ’s Pathogen Detection websites with simple keywords
We’ve redesigned the filters on NCBI’s Pathogen Detection websites to make searching easier! For example, say you wanted to search for outbreak isolates related to flour. Before the filters were redesigned, you’d have to know that some of the available metadata terms include “flour”, “All-purpose Wheat flour”, and “wheat flour”, along with seventeen other terms. … Continue reading Search NCBI’s Pathogen Detection websites with simple keywords → (Source: NCBI Insights)
Source: NCBI Insights - November 19, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Pathogen Detection Source Type: news

BLAST+ 2.11.0 now available with limited usage reporting to help improve BLAST
BLAST+ 2.11.0 release is now available from our FTP site.  The main advance is the to provide usage reports to NCBI to help us improve BLAST.  This information is limited to the name of the BLAST program, some basic database metadata, a few BLAST parameters, as well the number and total size of your queries … Continue reading BLAST+ 2.11.0 now available with limited usage reporting to help improve BLAST → (Source: NCBI Insights)
Source: NCBI Insights - November 12, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

RefSeq Release 203 now available
RefSeq release 203 is now available online, from the FTP site and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of November 2, 2020, and contains 256,340,911 records, including 186,482,096 proteins, 34,176,314 RNAs, and sequences from 105,349 organisms. The release is provided in several directories as … Continue reading RefSeq Release 203 now available → (Source: NCBI Insights)
Source: NCBI Insights - November 12, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New RefSeq Source Type: news

Human GRCh37 (hg19)  RefSeq annotation update 
The NCBI RefSeq group has been in overdrive, making improvements to our human genome annotation and reference transcript and protein sets, with 8,000 new and 15,000 updated transcripts in the last year alone! That’s about 30% of our curated transcript dataset (the transcripts with NM_ and NR_ accessions), with a big focus on transcripts that are well-expressed, have … Continue reading Human GRCh37 (hg19) RefSeq annotation update  → (Source: NCBI Insights)
Source: NCBI Insights - November 12, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New genome annotation GRCh37 RefSeq Source Type: news

Genome Workbench Submission Wizard to replace Sequin for prokaryotic and eukaryotic genome submissions in January 2021
If you use Sequin to submit prokaryotic or eukaryotic genome sequences to GenBank, you need to be aware that Sequin will be retired in January 2021. Genome Workbench’s Submission Wizard, which is already available for submitting annotated genomes, will be the submission tool to use for annotated genomes going forward. Genome Workbench is desktop software … Continue reading Genome Workbench Submission Wizard to replace Sequin for prokaryotic and eukaryotic genome submissions in January 2021 → (Source: NCBI Insights)
Source: NCBI Insights - November 9, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New genome Genome Workbench sequin submissions Source Type: news

GenBank 240.0 is available and surpasses 10 trillion basepairs!
GenBank release 240.0 (10/28/2020) is now available on the NCBI FTP site. This release has 10.33 trillion bases and 2.17 billion records. The current release has 219,055,207 traditional records containing 698,688,094,046 base pairs of sequence data. There are also 1,432,874,252 WGS records containing 9,215,815,569,509 base pairs of sequence data, 435,968,379 bulk-oriented TSA records containing 382,996,662,270 … Continue reading GenBank 240.0 is available and surpasses 10 trillion basepairs! → (Source: NCBI Insights)
Source: NCBI Insights - November 5, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news

November 18 Webinar: A new way to prepare genome submissions using NCBI ’ s Genome Workbench!
Join us November 18 to learn how to use Genome Workbench, NCBI’s sequence annotation and analysis package, to prepare genome submissions for GenBank.  This webinar will help you prepare for the upcoming retirement of Sequin submission tool in January 2021. You will learn how to use Genome Workbench’s Submission Wizard, Validation and Submitter Reports, Flat … Continue reading November 18 Webinar: A new way to prepare genome submissions using NCBI’s Genome Workbench! → (Source: NCBI Insights)
Source: NCBI Insights - November 2, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

NCBI  RefSeq and Ensembl/GENCODE taking MANE mainstream with v0.92!
NCBI and EBI have been hard at work on our joint MANE collaboration, providing a set of representative transcripts for human protein-coding genes that are identically annotated in the NCBI RefSeq and Ensembl/GENCODE annotation sets and exactly match the GRCh38 reference assembly. We’re pleased to announce MANE v0.92, now covering 16,865 genes or ~88% of known human protein-coding genes. In particular, we’ve … Continue reading NCBI RefSeq and Ensembl/GENCODE taking MANE mainstream with v0.92! → (Source: NCBI Insights)
Source: NCBI Insights - November 2, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New ClinVar GRCh38 MANE Source Type: news

IgBLAST 1.17 is now available with improved identification of productive V gene sequences
A new release of IgBLAST (1.17), the popular package for classifying and analyzing immunoglobulin and T cell receptor sequences, is now available on the web and from the FTP site. The updated package is better at identifying productive V gene sequences. We added a new field , “V frame shift”, to the IgBLAST output to … Continue reading IgBLAST 1.17 is now available with improved identification of productive V gene sequences → (Source: NCBI Insights)
Source: NCBI Insights - October 30, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

New feature in the dbGap submission portal: Automated study metadata
dbGaP has recently released a new feature to simplify submissions and provide study accessions faster. This video provides a quick overview of the new feature.  Our new study config webform enables a study submitter to enter important study summary information including study description, inclusion/exclusion criteria, history, attribution, and associated publications online and instantly preview the study config … Continue reading New feature in the dbGap submission portal: Automated study metadata → (Source: NCBI Insights)
Source: NCBI Insights - October 29, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New dbgap Source Type: news

Programmatic access to Gene Data using Datasets command-line and API
In March, we announced NCBI Datasets, a new resource that lets you easily retrieve and download data from across NCBI databases. Did you know you can now fetch NCBI Gene data programmatically using the NCBI Datasets API or command-line tool?  Quickly retrieve both metadata and gene sequence data for multiple Gene records including transcripts and proteins … Continue reading Programmatic access to Gene Data using Datasets command-line and API → (Source: NCBI Insights)
Source: NCBI Insights - October 28, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New API datasets downloading data Gene Source Type: news

New RefSeq annotations for mouse, maize, sunflower and more!
In August and September, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms: Amphiprion ocellaris (clown anemonefish) Anopheles stephensi (Asian malaria mosquito) Aplysia californica (California sea hare) Bactrocera oleae (olive fruit fly) Branchiostoma floridae (Florida lancelet) Egretta garzetta (little egret) Folsomia candida (springtail) Fundulus heteroclitus (mummichog) Halichoerus grypus (gray seal) Helianthus … Continue reading New RefSeq annotations for mouse, maize, sunflower and more! → (Source: NCBI Insights)
Source: NCBI Insights - October 22, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New eukaryotic genome annotation RefSeq Source Type: news

New PubMed updates and retirement of legacy PubMed on October 31
The new PubMed has been the default now since May, and more than 99% of you are using the new site. The recent NLM technical bulletin has details on features that we have added to the new PubMed based on your requests. Legacy PubMed, which has been available in parallel with the new PubMed, will … Continue reading New PubMed updates and retirement of legacy PubMed on October 31 → (Source: NCBI Insights)
Source: NCBI Insights - October 21, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New biomedical literature PubMed Source Type: news

Structure viewer iCn3D 2.20.0 is available with new features including viewing an electrostatic potential map!
The NCBI structure viewer iCn3D 2.20.0 is now available on the NCBI web site and from GitHub. You can now view the electrostatic potential map for any subset of 3D structures within 30,000 atoms. The potential is calculated using the DelPhi program by solving a linear Poisson-Boltzmann equation. You can show the potential on a … Continue reading Structure viewer iCn3D 2.20.0 is available with new features including viewing an electrostatic potential map! → (Source: NCBI Insights)
Source: NCBI Insights - October 21, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New iCn3D Source Type: news

NCBI Presents Two Online CoLabs at ASHG 2020!
Two up-and-coming NCBI resources will be featured in videos, surveys and live events at the American Society for Human Genetics (ASHG) 2020 Annual Meeting. Come and watch on-demand videos in the CoLab Theater. Then, let us know what you think and how you do or might use these resources by either taking an online survey … Continue reading NCBI Presents Two Online CoLabs at ASHG 2020! → (Source: NCBI Insights)
Source: NCBI Insights - October 19, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New American Society for Human Genetics (ASHG) datasets dbgap dbGaP Allele Frequency Aggregator (ALFA) dbSNP dbVar Source Type: news

BLAST now offers RefSeq Select databases for faster searches and better results
RefSeq select offers a high-quality set of transcript and protein sequences for human and mouse; for prokaryotes,  RefSeq select is the set of proteins annotated on RefSeq reference and representative genomes. You can now search these sets on the nucleotide and protein BLAST services. The new databases are  RefSeq Select rna sequences and RefSeq Select proteins (Figure … Continue reading BLAST now offers RefSeq Select databases for faster searches and better results → (Source: NCBI Insights)
Source: NCBI Insights - October 16, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

Announcing the RefSeq annotation of mouse GRCm39!
NCBI RefSeq has finished its initial annotation of the new mouse reference assembly, GRCm39, recently released by the Genome Reference Consortium. This is the first coordinate-changing update to the mouse reference since the 2012 release of GRCm38, resolving over 400 issues, almost doubling the scaffold N50, closing almost half the gaps, and adding 1.9 Mb of sequence. It’s … Continue reading Announcing the RefSeq annotation of mouse GRCm39! → (Source: NCBI Insights)
Source: NCBI Insights - October 16, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GRCm39 RefSeq Source Type: news

NCBI Datasets now provides downloads of gene data for more than 30 thousand organisms
NCBI Datasets now offers Gene tables: customizable tables of the genes you specify, with key gene information, and the ability to easily download a dataset of genomic, transcript and protein sequences. Drag and drop a list of Gene IDs or gene symbols, and the data table shows your genes with up to 15 columns of metadata, … Continue reading NCBI Datasets now provides downloads of gene data for more than 30 thousand organisms → (Source: NCBI Insights)
Source: NCBI Insights - October 9, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New datasets downloading data Gene RefSeq Source Type: news

Recent enhancements in Genome Workbench version 3.5.0
New Features Version 3.5.0 of Genome Workbench, NCBI’s sequence annotation and analysis platform, includes two new features.  First, we improved the phylogenetic reconstruction algorithm to add sequence additional meta-information, such as isolation source, collection date, and country. This is useful for analyzing coronaviruses, for example.  For more information on this feature, check out our new tutorials: … Continue reading Recent enhancements in Genome Workbench version 3.5.0 → (Source: NCBI Insights)
Source: NCBI Insights - October 8, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Genome Workbench Source Type: news

The latest in COVID-19 related human gene annotation now in NCBI RefSeq and Gene
Interested in human genes involved in COVID-19 biology? NCBI’s RefSeq group has been hard at work compiling a set of human genes with roles in coronavirus infection and disease. You can now see and search for these genes and their regulatory elements in NCBI Gene and RefSeq. Figure 1. Top section of the human ACE2 record in the Gene database. COVID-19 … Continue reading The latest in COVID-19 related human gene annotation now in NCBI RefSeq and Gene → (Source: NCBI Insights)
Source: NCBI Insights - October 2, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New COVID-19 Gene RefSeq RefSeq Functional Elements SARS-CoV-2 Source Type: news

Oct 14 webinar: Exploring SRA Metadata with AWS Athena and a new dataset for SARS-CoV-2
Join us on Oct 14th to learn how to use Athena on AWS to quickly search Sequence Read Archive (SRA) in the cloud to speed up your bioinformatic research and discovery projects and to explore a new SRA SARS-CoV-2 dataset. In this webinar, we’ll introduce you to a way to search SRA submitter-supplied metadata and … Continue reading Oct 14 webinar: Exploring SRA Metadata with AWS Athena and a new dataset for SARS-CoV-2 → (Source: NCBI Insights)
Source: NCBI Insights - September 30, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

Oct 14 webinar: Exploring SRA Metadata with AWS Athena, including a new dataset for SARS-CoV-2
Join us on Oct 14th to learn how to use Athena on AWS to quickly search Sequence Read Archive (SRA) in the cloud to speed up your bioinformatic research and discovery projects and to explore a new SRA SARS-CoV-2 dataset. In this webinar, we’ll introduce you to a way to search SRA submitter-supplied metadata and … Continue reading Oct 14 webinar: Exploring SRA Metadata with AWS Athena, including a new dataset for SARS-CoV-2 → (Source: NCBI Insights)
Source: NCBI Insights - September 30, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

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 → (Source: NCBI Insights)
Source: NCBI Insights - September 25, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New BLAST Primer-BLAST Sequence Viewer Source Type: news

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 → (Source: NCBI Insights)
Source: NCBI Insights - September 18, 2020 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Genome Browser Genome Data Viewer (GDV) Sequence Viewer Source Type: news