Participating labs contribute over 70 tests for COVID-19 to the NIH Genetic Testing Registry
During the COVID-19 pandemic, an often-heard refrain in the arena of public health was “Testing, testing, testing!”. Testing for the presence of the SARS-CoV-2 virus in patients with symptoms or potential exposure, or for the presence of antibodies to the virus in patients who had recovered from the disease, took on vital importance in efforts … Continue reading Participating labs contribute over 70 tests for COVID-19 to the NIH Genetic Testing Registry → (Source: NCBI Insights)
Source: NCBI Insights - July 22, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New COVID-19 Source Type: news

New RefSeq annotations for human, zebra finch, great white shark and more!
In May and June, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for 27 organisms. This release includes new annotations for human, zebra finch, golden eagle, sea urchin, snowfinch, Arctic fox, clawed frog, great white shark, and more: Alosa sapidissima (American shad) Anopheles merus (mosquito) Aquila chrysaetos chrysaetos (golden eagle) Aricia agestis (brown argus) … Continue reading New RefSeq annotations for human, zebra finch, great white shark and more! → (Source: NCBI Insights)
Source: NCBI Insights - July 21, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation RefSeq Source Type: news

RefSeq release 207 is available!
RefSeq release 207 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 July 12, 2021, and contains 285,425,070 records, including 209,035,492 proteins, 39,039,901 RNAs, and sequences from 112,462 organisms. The release is provided in several directories as a complete dataset … Continue reading RefSeq release 207 is available! → (Source: NCBI Insights)
Source: NCBI Insights - July 16, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets Eukaryotic genome annotation NCBI Prokaryotic Genome Annotation Pipeline (PGAP) RefSeq Source Type: news

Updates on SARS-CoV-2 resources and cloud data services at ASV 2021
NCBI staff will be presenting  talks and a poster on accessing SARS-CoV-2 at NCBI and in the Cloud at the American Society of Virology 2021 virtual conference, July 19-23, 2021. Presentations July 19, 2021, 6:00PM to 9:30PM, Epidemiology and Public Health Eneida Hatcher, Ph.D.,  will present ‘Providing an easy-to-use, graphics driven interface for normalized public SARS-CoV-2 … Continue reading Updates on SARS-CoV-2 resources and cloud data services at ASV 2021 → (Source: NCBI Insights)
Source: NCBI Insights - July 15, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New ASV2021 Cloud computing Coronavirus SARS-CoV-2 Sequence Read Archive (SRA) Source Type: news

Introducing the new NCBI Datasets Genomes page
The updated NCBI Datasets Genomes page now has genome data for all domains of life, including bacterial and viral genomes. The genomes table (Figure 1) now offers filters for: Reference genomes — switch it on to only show reference or representative genomes Annotated — switch it on to only show annotated genomes Assembly level — use the assembly level … Continue reading Introducing the new NCBI Datasets Genomes page → (Source: NCBI Insights)
Source: NCBI Insights - July 14, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly Basic Local Alignment Search Tool (BLAST) Datasets Genome Genome assemblies Genome Data Viewer (GDV) Source Type: news

July 28 Webinar: An update on native NCBI password retirement
The password you set at NCBI to log in to My NCBI, SciENcv, My Bibliography, or submit data to NCBI, will be going away. You will soon have to link a third-party login (e.g. eRA Commons, Google, Microsoft, or a university or institutional log in) to access your account. Join us on July 28, 2021 … Continue reading July 28 Webinar: An update on native NCBI password retirement → (Source: NCBI Insights)
Source: NCBI Insights - July 13, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New My Bibliography My NCBI SciENcv Submissions Webinars Source Type: news

BLAST+ 2.12.0 now available with more efficient multithreaded searches
BLAST+ 2.12.0  programs feature better multithreaded searches and support a different threading model, threading by query, that can be more efficient in some situations.  The new release is also fully compatible the increase in the numeric range for the GI identifier, which will take effect in the nucleotide database later this year.  The list below … Continue reading BLAST+ 2.12.0 now available with more efficient multithreaded searches → (Source: NCBI Insights)
Source: NCBI Insights - July 9, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Nucleotide BLAST (blastn) Protein BLAST (BLASTp) Source Type: news

Codeathon from the Couch — NCBI North Texas Workshops and Codeathon 2021
The NCBI North Texas Workshops and Codeathon 2021 finished with a three-day online, interactive codeathon. Codeathons help solve biological problems by fostering collaborative environments for attendees to create new computational tools and are a great learning, networking, and project development experience for scientists at any stage in their career. One team leader from the NCBI … Continue reading Codeathon from the Couch — NCBI North Texas Workshops and Codeathon 2021 → (Source: NCBI Insights)
Source: NCBI Insights - July 6, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

NCBI to present on SRA and cloud computing at the 2021 Galaxy Community Conference
We’re bringing exciting developments to our user community at the 2021 Galaxy Community Conference (GCC 2021), which is virtual this year!                     We start with hosting NCBI’s first ever GCC training week tutorial co-written by Jon Trow, Ph.D. – Sequence Read Archive (SRA): Subject Matter Expert … Continue reading NCBI to present on SRA and cloud computing at the 2021 Galaxy Community Conference → (Source: NCBI Insights)
Source: NCBI Insights - July 1, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Cloud computing Conferences Sequence Read Archive (SRA) Source Type: news

GenBank release 244.0
(6/26/2021) is now available on the NCBI FTP site. This release has 14.78 trillion bases and 2.46 billion records. The current release has 227,888,889 traditional records containing 866,009,790,959 base pairs of sequence data. There are also 1,632,796,606 WGS records containing 13,442,974,346,437 base pairs of sequence data, 494,641,358 bulk-oriented TSA records containing 436,594,941,165 … Continue reading GenBank release 244.0 → (Source: NCBI Insights)
Source: NCBI Insights - June 30, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news

Announcing the re-annotation of RefSeq genome assemblies for E. coli and four other species!
We have re-annotated all RefSeq genomes for Escherichia coli, Mycobacterium tuberculosis, Bacillus subtilis, Acinetobacter pittii, and Campylobacter jejuni using the most recent release of PGAP. You will find that more genes now have gene symbols (e.g. recA). Your feedback indicated that the lack of symbols was an impediment to comparative analysis, so we hope that this improvement … Continue reading Announcing the re-annotation of RefSeq genome assemblies for E. coli and four other species! → (Source: NCBI Insights)
Source: NCBI Insights - June 23, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Genome annotation Genome assemblies NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Reference genome RefSeq Source Type: news

June 30 Webinar: Using NCBI Datasets to download sequence and annotation for genomes and genes
Join us on June 30, 2021 at 12PM eastern time to learn how to use the new NCBI Datasets resource to find and download gene, genome and SARS-CoV-2 sequence and annotation. You will learn how to access these datasets through either the web interface or the new command-line tools that allow you to incorporate these data … Continue reading June 30 Webinar: Using NCBI Datasets to download sequence and annotation for genomes and genes → (Source: NCBI Insights)
Source: NCBI Insights - June 22, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets Downloading data SARS-CoV-2 Webinars Source Type: news

Getting Started with Python and Cloud Computing — NCBI North Texas Workshops and Codeathon 2021
Learning to use computational tools and techniques is increasingly important for life scientists. But knowing where to start when learning relevant data-centric skills such as coding and cloud computing can be a big challenge. The NCBI education team is here to help!  As a part of the NCBI North Texas Workshops and Codeathon, we presented … Continue reading Getting Started with Python and Cloud Computing — NCBI North Texas Workshops and Codeathon 2021 → (Source: NCBI Insights)
Source: NCBI Insights - June 22, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

New version of PGAP available now!
We are happy to announce that a new version of PGAP is available. This version will annotate 20 to 25% more genes with symbols (e.g. recA) on the assembled genomes of key species, compared to previous versions. You will observe an increase in symbols when you annotate the genomes of Escherichia coli, Campylobacter jejuni and … Continue reading New version of PGAP available now! → (Source: NCBI Insights)
Source: NCBI Insights - June 15, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Source Type: news

Structure viewer iCn3D version 3 featuring analysis of 3D structures!
The NCBI structure viewer iCn3D version 3 is now available on the NCBI web site and from GitHub. Analysis of 3D Structures You can use the current version with the icn3d package at npm to write scripts to call functions in iCn3D. For example, this script on GitHub can calculate the change in interactions due to … Continue reading Structure viewer iCn3D version 3 featuring analysis of 3D structures! → (Source: NCBI Insights)
Source: NCBI Insights - June 11, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New iCn3D NCBI Structure SARS-CoV-2 Source Type: news

Automate your workflow with the ClinVar Submission API
ClinVar and our scientific and patient-care community rely on your submissions. With our new Application Programming Interface (API) for submissions, we’ve made it even easier for you to provide us with your most up-to-date classification of variants. The new RESTful API allows you to automate your submission workflow so that you can submit new records … Continue reading Automate your workflow with the ClinVar Submission API → (Source: NCBI Insights)
Source: NCBI Insights - June 11, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New API ClinVar Source Type: news

ClinVar Reaches One Million Variants!
ClinVar has become a go-to resource for the clinical genetics community.  You have come to ClinVar to look for the reported clinical significance of human genetic variants that you’ve identified in clinical testing or through your research.  You have researched the supporting evidence and publications to the benefit of the health and genetic science community .  … Continue reading ClinVar Reaches One Million Variants! → (Source: NCBI Insights)
Source: NCBI Insights - June 4, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New ClinVar Source Type: news

GenBank release 243.0
(5/26/2021) is now available on the NCBI FTP site. This release has 14.03 trillion bases and 2.40 billion records. The current release has 227,123,201 traditional records containing 832,400,799,511 base pairs of sequence data. There are also 1,590,670,459 WGS records containing 12,732,048,052,023 base pairs of sequence data, 481,154,920 bulk-oriented TSA records containing 425,076,483,459 … Continue reading GenBank release 243.0 → (Source: NCBI Insights)
Source: NCBI Insights - June 3, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news

A more modern PMC is coming – let us know what you think in PMC Labs!
We’re updating PubMed Central (PMC) to a give you a more modern and easier to use site and we want your feedback. The first phase of this work is now on PMC Labs  for you to explore and provide feedback. In the first phase we have focused on modernizing PMC’s platform to create a more … Continue reading A more modern PMC is coming – let us know what you think in PMC Labs! → (Source: NCBI Insights)
Source: NCBI Insights - June 2, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Biomedical literature NCBI Labs PubMed Central (PMC) Source Type: news

Work(shops) from home – NCBI North Texas Workshops and Codeathon 2021
The NCBI Education team worked with universities in the greater Dallas area to host and present four online workshops and a codeathon, May 11th-20th. These events helped attendees from a variety of educational backgrounds and interests incorporate NCBI data and tools into their work. The NCBI North Texas Workshops spanned topics of clinical genetics, human … Continue reading Work(shops) from home – NCBI North Texas Workshops and Codeathon 2021 → (Source: NCBI Insights)
Source: NCBI Insights - June 1, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

Announcing RefSeq Release 206!
RefSeq Release 206 is now available. This release includes the following: Updated human genome Annotation Release 109.20210514 Updated Annotation Release 109.20210514 is an update of NCBI Homo sapiens Annotation Release 109. The annotation report is available here. The annotation products are available in the sequence databases and on the FTP site. Other new eukaryotic genome … Continue reading Announcing RefSeq Release 206! → (Source: NCBI Insights)
Source: NCBI Insights - May 27, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation Human genome Prokaryotic genome annotation Read assembly and Annotation Pipeline Tool (RAPT) RefSeq Source Type: news

The wait is over … NIH ’s Public Sequence Read Archive is now open access on the cloud
The NIH NCBI Sequence Read Archive (SRA) on AWS, containing all public SRA data, is now live! This data is hosted on Amazon Web Services (AWS) under the Open Data Sponsorship Program (ODP) with support from NIH’s Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) initiative. The SRA is NIH’s primary repository for raw, … Continue reading The wait is over… NIH’s Public Sequence Read Archive is now open access on the cloud → (Source: NCBI Insights)
Source: NCBI Insights - May 27, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Cloud computing Open data Sequence Read Archive (SRA) STRIDES Source Type: news

Introducing GaPTools, a stand-alone data validation tool for dbGaP submissions
We have just launched GaPTools, a stand-alone data validation tool for NCBI’s database of Genotype and Phenotype (dbGaP) submissions. You can use GaPTools to validate your dbGaP submissions or submissions to other genomic data repositories. GaPTools checks for common data inconsistency and integrity issues and validates subject-sample ID mapping, subject consents, data dictionaries, and phenotype … Continue reading Introducing GaPTools, a stand-alone data validation tool for dbGaP submissions → (Source: NCBI Insights)
Source: NCBI Insights - May 26, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Database of Genotypes and Phenotypes (dbGaP) GaPTools Source Type: news

June 2 Webinar: Quickly upload and view your own data in genomic context at NCBI
Join us on June 2, 2021 at 12PM eastern time to learn how to how to upload and display your own genomic data in the context of annotated genome assemblies. You will use the Genome Data Viewer and the Sequence viewer to visualize your own uploaded data (indexed BAM, VCF, BED, wig, GFF formats), data … Continue reading June 2 Webinar: Quickly upload and view your own data in genomic context at NCBI → (Source: NCBI Insights)
Source: NCBI Insights - May 21, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Genome Data Viewer (GDV) Primer-BLAST Sequence Viewer Webinars Source Type: news

Magic-BLAST version 1.6.0 is here!
We’ve just released  a new version (1.6.0) of Magic-BLAST, the BLAST-based next-gen alignment tool, with these improvements: Usage reporting — you can help improve Magic-BLAST by sharing limited information about your search. The BLAST User Manual has details on the information collected, how it is used, and how to opt-out. Magic BLAST can access NCBI … Continue reading Magic-BLAST version 1.6.0 is here! → (Source: NCBI Insights)
Source: NCBI Insights - May 18, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) DNA-Seq Magic-BLAST Next-gen sequencing (NGS) RNA-Seq Sequence Read Archive (SRA) Source Type: news

Vertebrate Genome Project genome assemblies annotated by NCBI
NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species.  See the VGP press release  for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank  and the … Continue reading Vertebrate Genome Project genome assemblies annotated by NCBI → (Source: NCBI Insights)
Source: NCBI Insights - May 17, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly Datasets Eukaryotic genome annotation GDH Genome Data Viewer (GDV) NCBI Nucleotide Protein Source Type: news

Prokaryotic representative genomes update – over 900 new species!
We are happy to announce an updated bacterial and archaeal representative genome collection! We have selected 13,835 among 214,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 6% since December 2020. About 950 species are represented for the first time, 476 species are represented by a better assembly, and 170 … Continue reading Prokaryotic representative genomes update–over 900 new species! → (Source: NCBI Insights)
Source: NCBI Insights - May 13, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Nucleotide BLAST (blastn) Prokaryotic genome annotation Representative genome Source Type: news

Assemble and annotate your prokaryotic genomes with RAPT
Do you need an easy way to analyze a bacterium you just isolated? The Read assembly and Annotation Pipeline Tool (RAPT) is a pilot service for the assembly and gene annotation of public or private Illumina genomic reads sequenced from bacterial or archaeal isolates. We’ll be giving a webinar on webRAPT on May 19, but … Continue reading Assemble and annotate your prokaryotic genomes with RAPT → (Source: NCBI Insights)
Source: NCBI Insights - May 12, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Read assembly and Annotation Pipeline Tool (RAPT) Source Type: news

May 19 Webinar: Using the new web RAPT service to assemble and annotate prokaryotic genomes
Join us on May 19, 2021 at 12PM eastern time to learn how to use the new  RAPT pilot service to assemble and annotate public or private Illumina genomic reads sequenced from bacterial or archaeal isolates at the click of a button. RAPT consists of two major components, the genome assembler SKESA and the Prokaryotic Genome … Continue reading May 19 Webinar: Using the new web RAPT service to assemble and annotate prokaryotic genomes → (Source: NCBI Insights)
Source: NCBI Insights - May 12, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New DNA-Seq NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Next-gen sequencing (NGS) Read assembly and Annotation Pipeline Tool (RAPT) Sequence Read Archive (SRA) SKESA Webinars Source Type: news

A dedicated SARS-CoV-2 BioSample submission package in the NCBI Submission Portal
During the COVID-19 pandemic, it is critical to collect descriptive information about the provenance and attributes of SARS-CoV-2 genomic samples so that the course of the virus may be tracked and analyzed. The NCBI Submission Portal now includes a dedicated BioSample submission package to help further improve the quality and richness of submitted SARS-CoV-2 sample … Continue reading A dedicated SARS-CoV-2 BioSample submission package in the NCBI Submission Portal → (Source: NCBI Insights)
Source: NCBI Insights - May 11, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New SARS-CoV-2 Submissions Source Type: news

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021
NCBI staff will be presenting virtual posters at the Cold Spring Harbor Laboratory  Biology of Genomes Meeting, May 11 -14, 2021. The posters will cover the following topics: 1) a cloud-ready suite of tools (PGAP, RAPT , and SKESA) for assembling and annotating prokaryotic genomes,  2) Datasets — a new set of services for downloading … Continue reading NCBI at CSHL Biology of Genomes, May 11 – 14, 2021 → (Source: NCBI Insights)
Source: NCBI Insights - May 7, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Conferences Datasets Eukaryotic genome annotation GDH NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Read assembly and Annotation Pipeline Tool (RAPT) RefSeq SKESA Source Type: news

NCBI on YouTube: Tips for My Bibliography, Genome Data Viewer and more
Missed our latest YouTube videos? Scroll down to see what we’ve been up to. Add Preprint Citations in My Bibliography The National Institutes of Health encourages investigators to post preprints to public repositories in order to speed the dissemination and enhance the rigor of their work. This video demonstrates how to add preprint citations to … Continue reading NCBI on YouTube: Tips for My Bibliography, Genome Data Viewer and more → (Source: NCBI Insights)
Source: NCBI Insights - May 6, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Genome Data Viewer (GDV) My Bibliography My NCBI Primer-BLAST YouTube Source Type: news

New RefSeq annotations for Siamese fighting fish, common toad, swan, platypus and more!
In March and April, the NCBI Eukaryotic Genome Annotation Pipeline released thirty-two new annotations in RefSeq for the following organisms: Aegilops tauschii (monocot) Amblyraja radiata (thorny skate) Anopheles arabiensis (mosquito) Anopheles coluzzii (mosquito) Bactrocera tryoni (Queensland fruit fly) Belonocnema kinseyi (wasp) Betta splendens (Siamese fighting fish) Bufo bufo (common toad) Cygnus olor (mute swan) Falco naumanni (lesser kestrel) … Continue reading New RefSeq annotations for Siamese fighting fish, common toad, swan, platypus and more! → (Source: NCBI Insights)
Source: NCBI Insights - May 5, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation RefSeq Source Type: news

Assembly database passes 1 million genome assemblies!
The NCBI Assembly database now provides sequence and metadata for more than 1 million genome assemblies from over 85,000 different species. Assembly crossed the 1 million genome assemblies milestone on Sunday, April 18, 2021 (Figure 1). Figure 1. Assembly status and growth. More than 1 million assemblies are now searchable through the NCBI web site (top panel). … Continue reading Assembly database passes 1 million genome assemblies! → (Source: NCBI Insights)
Source: NCBI Insights - April 30, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly Genome assemblies NCBI Pathogen Detection Source Type: news

Data for SARS-CoV-2 variants now available at NCBI
Looking for genomes for the B.1.1.7 SARS-CoV-2 variant? NCBI now supports searches for SARS-CoV-2 variant names such as B.1.1.7, B.1.351, or P.1. For example, search for B.1.1.7 (Figure 1) and you’ll see a virus classification box with an option to download a SARS-CoV-2 data package. SARS-CoV-2 data packages include genome and protein sequences and a … Continue reading Data for SARS-CoV-2 variants now available at NCBI → (Source: NCBI Insights)
Source: NCBI Insights - April 23, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets SARS-CoV-2 Source Type: news

New NCBI Datasets home and documentation pages provide easier access
NCBI Datasets, the new set of services for downloading genome assembly and annotation data (previous Datasets posts), has redesigned and reorganized web pages to make it easier to find and access the services and documentation you need. NCBI Datasets has a fresh new homepage (Figure 1) highlighting the types of data available through our tools. Available … Continue reading New NCBI Datasets home and documentation pages provide easier access → (Source: NCBI Insights)
Source: NCBI Insights - April 20, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets Downloading data Gene Genome annotation Genome assemblies SARS-CoV-2 Viruses Source Type: news

Remembering Mark Boguski
It is with much sadness that we recently learned of the passing of Mark Boguski, MD, PhD, a former Senior Investigator in the Computational Biology Branch at NCBI. Mark worked at the NCBI from 1989-2000 and made a lasting impression on the staff who are still with NCBI and who overlapped with his time here. … Continue reading Remembering Mark Boguski → (Source: NCBI Insights)
Source: NCBI Insights - April 14, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Boguski Source Type: news

April 7 Webinar: Recent and upcoming enhancements to NCBI BLAST and Primer-BLAST services!
Join us on April 7, 2021 at 12PM eastern time to learn about new web BLAST and Primer-BLAST enhancements that improve your BLAST experience. You’ll also see a preview of some planned improvements to the databases that make it easier to find relevant matches. Recent changes to web BLAST include added data columns on the … Continue reading April 7 Webinar: Recent and upcoming enhancements to NCBI BLAST and Primer-BLAST services! → (Source: NCBI Insights)
Source: NCBI Insights - March 29, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Nucleotide BLAST (blastn) Primer-BLAST Protein BLAST (BLASTp) Webinars Source Type: news

Conserved Domain Database version 3.19 is available!
The Conserved Domain Database (CDD) version 3.19 is now available. This version contains 3,148 new or updated NCBI-curated domains and now mirrors Pfam version 33.1 as well as models from the NCBIfam collection. We also included fine-grained classifications of the immunoglobulin, RRM, cytochrome P450, 7-transmembrane GPCRs, KH, calponin homology and C1 domain superfamilies. With this CDD release, we introduce model-specific word-score thresholds for the RPS-BLAST heuristics. These … Continue reading Conserved Domain Database version 3.19 is available! &rarr...
Source: NCBI Insights - March 17, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Conserved Domains Database (CDD) Source Type: news

January-February 2021 RefSeq annotations include dog, fly, rat
This January and February, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms: Benincasa hispida (wax gourd) Canis lupus familiaris (dog) Corvus cornix cornix (hooded crow) Crotalus tigris (tiger rattlesnake) Culex pipiens pallens (northern house mosquito) Dioscorea cayenensis subsp. rotundata (Guinea yam) Drosophila santomea (fly) Drosophila simulans (fly) Drosophila … Continue reading January-February 2021 RefSeq annotations include dog, fly, rat → (Source: NCBI Insights)
Source: NCBI Insights - March 16, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation RefSeq Source Type: news

RefSeq Release 205 is available!
RefSeq release 205 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 March 1, 2021, and contains 269,975,565 records, including 197,232,209 proteins, 36,514,168 RNAs, and sequences from 108,257  organisms. The release is provided in several directories as a complete dataset … Continue reading RefSeq Release 205 is available! → (Source: NCBI Insights)
Source: NCBI Insights - March 12, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Genome annotation Genome assemblies Genomics Human genome RefSeq Source Type: news

New class value and qualifier in GenBank release 242.0 accommodate circular RNA molecules
GenBank release 242.0 (2/16/2021) is now available on the NCBI FTP site and through Entrez and BLAST. This release has 13.49 trillion bases and 2.34 billion records. Growth between releases During the 57 days between the close dates for GenBank Releases 241.0 and 242.0, the ‘traditional’ portion of GenBank grew by 53,287,389,099 base pairs and … Continue reading New class value and qualifier in GenBank release 242.0 accommodate circular RNA molecules → (Source: NCBI Insights)
Source: NCBI Insights - March 8, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news

ClinicalTrials.gov updates the PRS Guided Tutorials, step-by-step instructions for data providers
The PRS Guided Tutorials provide step-by-step instructions to help data providers submit information to ClinicalTrials.gov and aims to reduce the number of quality-control reviews needed. The ClinicalTrials.gov team has updated the PRS Guided Tutorials to make them more useful in response to user feedback obtained through focus groups and survey responses over the past year. … Continue reading ClinicalTrials.gov updates the PRS Guided Tutorials, step-by-step instructions for data providers → (Source: NCBI Insights)
Source: NCBI Insights - March 8, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New ClinicalTrials.gov Source Type: news

March 10 Webinar: Where to find data for your research organism!
Do you work with data from organisms outside the traditional set of model organisms? Join us on March 10, 2021 to learn how to use NCBI resources including NCBI’s Taxonomy and BLAST that can help you find information from your organism and closely related taxa. You will see an example that shows you how to … Continue reading March 10 Webinar: Where to find data for your research organism! → (Source: NCBI Insights)
Source: NCBI Insights - March 1, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) NCBI Taxonomy Primer-BLAST Webinars Source Type: news

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