New PGAP release: Structural and functional annotation improvements
A new version of the Prokaryotic Genome Annotation Pipeline (PGAP) is available on GitHub. With this release, you can expect: Incremental improvements in structural annotation, driven by increased weight of GeneMarkS2+ ab initio models at loci with only weak evidence, such as low identity and low coverage protein alignments or partial HMM signatures. Better structural … Continue reading New PGAP release: Structural and functional annotation improvements → (Source: NCBI Insights)
Source: NCBI Insights - December 3, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Hidden Markov Models (HMM) NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Source Type: news

New models added to the NCBI Hidden Markov models (HMM) collection with release 7.0
Release 7.0 of the NCBI Hidden Markov models (HMM), used by the Prokaryotic Genome Annotation Pipeline (PGAP), is now available for download. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. Figure 1. Recently added HMM-based Protein Family Model for the histidine-histamine antiporter family … Continue reading New models added to the NCBI Hidden Markov models (HMM) collection with release 7.0 → (Source: NCBI Insights)
Source: NCBI Insights - December 3, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Hidden Markov Models (HMM) HMMER NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Source Type: news

NCBI genome browsers: search and you will find!
If you’ve ever tried searching for a genomic location in NCBI’s Genome Data Viewer (GDV) or Variation Viewer and found that your search term didn’t work, it’s time to try again! We recently expanded support for searches in our genome browsers using non-NCBI identifiers such as HGVS patterns (e.g. NM_001318787.2:c.2258G>A) and Ensembl IDs. You can also search by chromosome coordinates, cytogenetic band, assembly scaffold/component, disease/phenotype, dbSNP … Continue reading NCBI genome browsers: search and you will find! → (Source: NCBI Insights)
Source: NCBI Insights - November 19, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Database of human genomic structural variation (dbVar) Genome Browser Genome Data Viewer (GDV) Single Nucleotide Polymorphism Database (dbSNP) Variation Viewer Source Type: news

NCBI on YouTube: Customize MSA Viewer, SciENcv, plants and RNA-Seq data, Datasets and PubMed
Missed a few videos on YouTube? Here’s the latest from our channel. Customize the MSA Viewer to Make Your Analysis Easier We’re constantly improving the Multiple Sequence Alignment (MSA) Viewer. This video demonstrates several new and popular features, including the ability to change data columns, hide selected rows, analyze polymorphisms, and more. An Update to … Continue reading NCBI on YouTube: Customize MSA Viewer, SciENcv, plants and RNA-Seq data, Datasets and PubMed → (Source: NCBI Insights)
Source: NCBI Insights - November 16, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Biosketch Datasets e-utilities Multiple Sequence Alignment Viewer (MSAV) PubMed RNA-Seq SciENcv Sequence Read Archive (SRA) YouTube Source Type: news

Web IgBLAST can now determine immunoglobulin isotypes
We have added a new function to IgBLAST on the Web. You can now search immunoglobulin (Ig) nucleotide sequences against the Constant region (C) gene database (Figure 1) to determine the Ig isotypes including subtypes (IgM, IgG, IgA1, etc.). The isotype information is reported in the rearrangement summary table, and the C gene region is … Continue reading Web IgBLAST can now determine immunoglobulin isotypes → (Source: NCBI Insights)
Source: NCBI Insights - November 16, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Immunoglobin Immunoglobulin and T cell receptor BLAST (IgBLAST) Source Type: news

GenBank release 246.0
(11/2/2021) is now available on the NCBI FTP site. This release has 16.1 trillion bases and 2.57 billion records. The current release has 233642893 traditional records containing 1,014,763,752,113 base pairs of sequence data. There are also 1,721,064,101 WGS records containing 14,599,101,574,547 base pairs of sequence data, 508,319,391 bulk-oriented TSA records containing 449,891,016,597 … Continue reading GenBank release 246.0 → (Source: NCBI Insights)
Source: NCBI Insights - November 15, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news

RefSeq Release 209 is available
RefSeq release 209 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 1, 2021, and contains 296,293,486 records, including 215,655,378 proteins, 41,751,205 RNAs, and sequences from 114,396  organisms. The release is provided in several directories as a complete … Continue reading RefSeq Release 209 is available → (Source: NCBI Insights)
Source: NCBI Insights - November 12, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation GenInfo Identifier (GI) RefSeq Sequences Source Type: news

A more modern PMC is on its way – there ’ s still time to give us feedback!
In June, we announced the arrival of PMC Labs, where you can test drive the work underway to create a more modern PMC website. Since then, we’ve continued to talk to users, gather input, and make ongoing adjustments based on your feedback. We hope that the planned updates will create an easier navigation and reading … Continue reading A more modern PMC is on its way – there’s still time to give us feedback! → (Source: NCBI Insights)
Source: NCBI Insights - November 8, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New PubMed Central (PMC) Source Type: news

NCBI ’ s Genome Data viewer now displays both NCBI RefSeq and submitted assemblies
NCBI’s Genome Data Viewer (GDV) now supports visualization and analysis of nearly 400 submitter-annotated chromosome-level assemblies from the INSDC (GenBank/ENA/DDBJ). These submitter-annotated assemblies join more than 1,200 NCBI RefSeq-annotated assemblies available in GDV for hundreds of eukaryotes, spanning fungi, plants, fish, insects, and all major model organisms. Figure 1 shows a GenBank apple assembly (GCA_004115385) … Continue reading NCBI’s Genome Data viewer now displays both NCBI RefSeq and submitted assemblies → (Source: NCBI Insights)
Source: NCBI Insights - November 7, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly CGR GDH GDV Genome Data Viewer (GDV) International Nucleotide Sequence Database Collaboration (INSDC) Source Type: news

Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV
The Genome Data Viewer (GDV) is now the comprehensive NCBI genome browser. The  development of GDV led to a few different types of genome browsers along the way, each one originally delivering visual displays for particular datasets. We developed the 1000 Genomes Browser for variation data from the 1000 Genomes project, the dbGaP Data Browser … Continue reading Three outdated browsers (1000 Genomes, dbGaP Data, and Get-RM) to retire in April 2022. Data available in GDV → (Source: NCBI Insights)
Source: NCBI Insights - October 28, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New 1000 Genomes Database of Genotypes and Phenotypes (dbGaP) GDH Genome Browser Genome Data Viewer (GDV) Human variant data Source Type: news

NCBI will assign 64-bit numeric GIs by November 15th. Update affected software!
As announced  last month, NCBI will begin assigning larger (64-bit) numeric ‘GIs’ to the remaining sequence types that still receive these identifiers. This change is expected as soon as Nov. 15th, 2021 but could occur earlier if data submission volumes are unexpectedly high. This is a reminder that all organizations and developers using our products should review software for any remaining … Continue reading NCBI will assign 64-bit numeric GIs by November 15th. Update affected software! → (Source: NCBI Insights)
Source: NCBI Insights - October 27, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Accession.version GenInfo Identifier (GI) NCBI Nucleotide Protein Records Sequences Source Type: news

Nov 3 Webinar: dbGaP submission improvements and GaPTools
Attention dbGaP submitters! Join us on November 3, 2021 at 12PM US eastern time to learn about data submission and processing improvements to dbGaP, NIH’s database of Genotype and Phenotype, which contains individual-level data associated with human research studies. You will see how we have made submission easier through the Submission Portal using automated preliminary … Continue reading Nov 3 Webinar: dbGaP submission improvements and GaPTools → (Source: NCBI Insights)
Source: NCBI Insights - October 25, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Database of Genotypes and Phenotypes (dbGaP) Human variant data Submissions Variation Source Type: news

View GEO, SRA, or dbGaP data tracks in NCBI ’ s Genome Data Viewer
Did you know that you can see epigenomic or other experimental data in NCBI’s Genome Data Viewer (GDV)? You can easily add aligned study results from GEO, SRA, and dbGaP as data tracks to GDV browser view. Just go to the Tracks button on the toolbar and select the menu option to Configure Tracks. Navigate … Continue reading View GEO, SRA, or dbGaP data tracks in NCBI’s Genome Data Viewer → (Source: NCBI Insights)
Source: NCBI Insights - October 21, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Database of Genotypes and Phenotypes (dbGaP) Gene Expression Omnibus (GEO) Genome Data Viewer (GDV) Genome-wide association studies (GWAS) RNA-Seq Sequence Read Archive (SRA) Single Nucleotide Polymorphism Database (dbSNP) Source Type: news

New NCBI Gene Ensembl Comparison Expansion
NCBI Gene has added Ensembl Rapid Releases to the calculation of matching annotations between NCBI RefSeq and Ensembl. This has resulted in the inclusion of over 60 additional assemblies for a total of 241 organisms represented in the set. Matches are made based on transcript and CDS comparisons, and Ensembl gene, transcript, and protein identifiers for annotations … Continue reading New NCBI Gene Ensembl Comparison Expansion → (Source: NCBI Insights)
Source: NCBI Insights - October 21, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Gene RefSeq Source Type: news

Bulk Sequence-Cytogenetic Conversion Service to be retired in April 2022
The Bulk Sequence-Cytogenetic Conversion Service tool at NCBI will be retired in April 2022. This tool obtained cytogenetic locations for a list of annotated genes, SNPs, or assembly coordinates from human, fruit fly, mouse, or rat genomes. It also obtained sequence coordinates for cytogenetic locations for these genomes. This web service will be retired due to low … Continue reading Bulk Sequence-Cytogenetic Conversion Service to be retired in April 2022 → (Source: NCBI Insights)
Source: NCBI Insights - October 20, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Genome annotation Genome Data Viewer (GDV) Genome Decoration Source Type: news

The Sequence Read Archive slims down your data with SRA Lite
In response to your requests for compact and faster-to-deliver data, NIH’s Sequence Read Archive (SRA) now offers a new data format – SRA Lite (Figure 1).  SRA Lite supports reliable and faster data transfer, downloads, and analysis using current tools. SRA Lite replaces the submitted base quality score (BQS) with a simplified read quality score, … Continue reading The Sequence Read Archive slims down your data with SRA Lite → (Source: NCBI Insights)
Source: NCBI Insights - October 19, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New DNA-Seq Next-gen sequencing (NGS) RNA-Seq Sequence Read Archive (SRA) SRA Toolkit Source Type: news

ClinVar annotations now available in NCBI Genome Browsers
Do you need to know which of the many NCBI dbSNP variants annotated near your region of interest are likely to be functionally or clinically significant? Figure it out with the track labelled  ‘ClinVar variants with precise endpoints’, available on sequence display viewers at NCBI, including the Genome Data Viewer (GDV) and Variation Viewer! This track shows variation … Continue reading ClinVar annotations now available in NCBI Genome Browsers → (Source: NCBI Insights)
Source: NCBI Insights - October 8, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: Quick Tips ClinVar Genome Data Viewer (GDV) Variation Viewer Source Type: news

Oct 20 Webinar: Introducing the updated PubMed E-utilities (API)
Join us on October 20, 2021 at 12PM US eastern time learn about an updated version of the E-utilities API for PubMed that we will launch on April 4, 2022. With few exceptions, this update will not change the E-utility URLs you currently use but will bring the search results up to date with the … Continue reading Oct 20 Webinar: Introducing the updated PubMed E-utilities (API) → (Source: NCBI Insights)
Source: NCBI Insights - October 7, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New API PubMed Webinars Source Type: news

New RefSeq annotations!
Since July, the NCBI Eukaryotic Genome Annotation Pipeline released fifty-four new annotations in RefSeq for the following organisms: Amphibalanus amphitrite (crustacean) Apis laboriosa (Himalayan honeybee) Bombus pyrosoma (bee) Callorhinchus milii (elephant shark) Carya illinoinensis (pecan) Catharus ustulatus (Swainson’s thrush) Centrocercus urophasianus (Greater sage-grouse) Cervus canadensis (even-toed ungulates) Cervus elaphus (red deer) Chelonia mydas (Green sea turtle) (pictured) Chiloscyllium plagiosum … Continue reading New RefSeq annotations! → (Source: NCBI Insights)
Source: NCBI Insights - October 7, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation RefSeq Source Type: news

Updated PubMed E-utilities coming in April 2022!
Do you develop an application that uses the PubMed API? Do you need to access PubMed data programmatically? Then you’ll be interested to know that we will be launching an updated version of the E-utilities API for PubMed on April 4, 2022. This updated version will align the functions of the E-utilities with the web … Continue reading Updated PubMed E-utilities coming in April 2022! → (Source: NCBI Insights)
Source: NCBI Insights - October 5, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New API e-utilities PubMed Source Type: news

A new service to evaluate the quality of your assembled genome!
Are you wondering about the quality of a human, mouse or rat genome that you have assembled? We offer a new service for evaluating the completeness, correctness, and base accuracy of your human, mouse or rat genome assembly compared to a reference assembly. You simply provide NCBI with one or more assemblies in FASTA format … Continue reading A new service to evaluate the quality of your assembled genome! → (Source: NCBI Insights)
Source: NCBI Insights - September 30, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly CGR Eukaryotic genome annotation Human genome Source Type: news

Updated prokaryotic representative genome collection
The bacterial and archaeal representative genome collection has been updated!  We selected a total of 14,912 of the 224,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has grown by 8% since April 2021 and now includes Candidatus and endosymbiont species (Figure 1), which constitute 303 and 140 respectively of the 1,077 newly … Continue reading Updated prokaryotic representative genome collection → (Source: NCBI Insights)
Source: NCBI Insights - September 30, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Nucleotide BLAST (blastn) Prokaryotic genome annotation RefSeq Source Type: news

NCBI Presentations at Biodiversity Genomics 2021 Highlight Growing Support for Comparative Genomics
The National Center for Biotechnology Information (NCBI) has several speakers at the upcoming Biodiversity Genomics Conference from September 27 to October 1, 2021. Valerie Schneider, head of NCBI’s SeqPlus Program and Deputy Director for Sequence Offerings, will present a poster discussing how NCBI’s new comparative genome research focus will enable researchers to explore all eukaryotic … Continue reading NCBI Presentations at Biodiversity Genomics 2021 Highlight Growing Support for Comparative Genomics → (Source: NCBI Insights)
Source: NCBI Insights - September 27, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Conferences Datasets RefSeq Source Type: news

New NCBI Virtual Workshop Series
We are excited to announce our new NCBI Virtual Workshop Series! This workshop series aims to engage and educate people who use NCBI resources for their biological/biomedical research, science education, and clinical application efforts. Our interactive, hands-on workshops are taught by experienced NCBI Education Faculty. The NCBI Education Team, which consists of researchers, educators, computer … Continue reading New NCBI Virtual Workshop Series → (Source: NCBI Insights)
Source: NCBI Insights - September 24, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Source Type: news

Four new options to simplify your SARS-CoV-2 submissions
We have recently added several exciting improvements to the SARS-CoV-2 GenBank submission process based on community feedback. To save you time, NCBI completes feature annotation for you, which means SARS-CoV-2 GenBank submission only requires a FASTA file and source metadata. Here are other new features to ease and simplify your submission workflow. Automatically remove failed … Continue reading Four new options to simplify your SARS-CoV-2 submissions → (Source: NCBI Insights)
Source: NCBI Insights - September 24, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank SARS-CoV-2 Submissions Source Type: news

NIH ’s Cloud Data Delivery Service: SRA Delivers Even More Big Data to your Cloud Bucket
The Sequence Read Archive (SRA) is the National Institute of Health’s (NIH) primary repository for raw, high-throughput sequencing data, containing both controlled- and open-access datasets that continue to grow exponentially. SRA is managed by the National Library of Medicine’s National Center for Biotechnology Information (NCBI), and the data are available from NCBI’s servers as well as through cloud platforms:  Amazon … Continue reading NIH’s Cloud Data Delivery Service: SRA Delivers Even More Big Data to your Cloud Bucket → (Source: NCBI Insights)
Source: NCBI Insights - September 23, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Cloud computing Sequence Read Archive (SRA) Source Type: news

Fungal Disease Awareness Week: fungal pathogen data and literature at NCBI
This post is in support of the CDC’s Fungal Disease Awareness Week — September 20-24, 2021. The impact of fungal diseases on human health has often been neglected, but increased association of fungal infections with severe illness and death during the COVID-19 pandemic has brought fungal diseases into the spotlight. According to the CDC, the … Continue reading Fungal Disease Awareness Week: fungal pathogen data and literature at NCBI → (Source: NCBI Insights)
Source: NCBI Insights - September 21, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Assembly COVID-19 Fungi PubMed RefSeq Source Type: news

RefSeq Release 208 is available!
RefSeq release 208 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 September 7, 2021, and contains 288,903,207 records, including 210,703,648 proteins, 40,213,945 RNAs, and sequences from 113,002 organisms. The release is provided in several directories as a complete dataset … Continue reading RefSeq Release 208 is available! → (Source: NCBI Insights)
Source: NCBI Insights - September 15, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation Genome assemblies Hidden Markov Models (HMM) RefSeq Source Type: news

New in NCBI Datasets: Species pages and species browser
NCBI Datasets introduces species pages and species browser! The species pages summarize taxon information and provide access to genomic data, including reference genomes. For example, see Figure 1, the Nothobranchius furzeri (turquoise killifish) species page. Figure 1: Nothobranchius furzeri species page. The browse species button will take you to the species browser.  From the species … Continue reading New in NCBI Datasets: Species pages and species browser → (Source: NCBI Insights)
Source: NCBI Insights - September 15, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets GDH Source Type: news

Learn the best way to find data in NIH ’s Sequence Read Archive (SRA) on the cloud
NCBI will present a workshop at the American Society for Human Genetics (ASHG) as part of their conference activities in 2021. The workshop is scheduled for Wednesday, September 15, 2021. Register now! Adelaide Rhodes, Ph.D. from the Customer Experience team and Adam Stine, SRA Curator will co-lead the workshop, which will introduce attendees to powerful … Continue reading Learn the best way to find data in NIH’s Sequence Read Archive (SRA) on the cloud → (Source: NCBI Insights)
Source: NCBI Insights - September 10, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Cloud computing Sequence Read Archive (SRA) Source Type: news

Sept 22 Webinar: Using NCBI Datasets command-line tools to access data and metadata for genomes
Join us on September 22, 2021 at 12PM eastern time learn to use the datasets command-line tools (datasets and dataformat) to access, filter, download, and format data and metadata for genomes. Through examples from eukaryotes and the SARS-CoV-2 coronavirus, you will see how to use metadata to filter for genome sequences with desired properties such … Continue reading Sept 22 Webinar: Using NCBI Datasets command-line tools to access data and metadata for genomes → (Source: NCBI Insights)
Source: NCBI Insights - September 8, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets GDH Genome assemblies Webinars Source Type: news

NCBI ’ s GI sequence identifiers will soon exceed 32-bit numbers. Are you and your software ready?
In 2016, NCBI announced that it was curtailing its display of its numeric ‘GI’ in popular sequence data formats such as FASTA and GenBank flatfiles. Due to the continued growth of GenBank, NCBI will soon begin assigning GIs exceeding the signed 32-bit threshold of 2,147,483,647 for those remaining sequence types that still receive these identifiers. The exact date … Continue reading NCBI’s GI sequence identifiers will soon exceed 32-bit numbers. Are you and your software ready? → (Source: NCBI Insights)
Source: NCBI Insights - September 2, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Accession.version GenInfo Identifier (GI) Records Sequences Source Type: news

PubMed Central Article Datasets are Now Available on the Cloud
To enhance machine access to biomedical literature and drive impactful analyses and reuse, the National Library of Medicine (NLM) is pleased to announce the availability of the PubMed Central (PMC) Article Datasets on Amazon Web Services (AWS) Registry of Open Data as part of AWS’s Open Data Sponsorship Program (ODP). These datasets collectively span 4 million of PMC’s 7 million … Continue reading PubMed Central Article Datasets are Now Available on the Cloud → (Source: NCBI Insights)
Source: NCBI Insights - September 1, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Cloud computing PubMed Central (PMC) Source Type: news

NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer
Every so often, we gather our most recent videos in one post on the blog, for your convenience. Scroll down – and don’t forget to subscribe to our channel! Introducing GaPTools for dbGaP Submitters This video introduces new standalone software called GaPTools, which you can use to check your data before submitting to dbGaP. GaPTools … Continue reading NCBI on YouTube: ClinVar API, check data with GaPTools, get genetic context with Sequence Viewer → (Source: NCBI Insights)
Source: NCBI Insights - August 27, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: Quick Tips API ClinVar GaPTools Genome Data Viewer (GDV) My NCBI Read assembly and Annotation Pipeline Tool (RAPT) Sequence Viewer Submissions Source Type: news

GenBank release 245.0
(8/18/2021) is now available on the NCBI FTP site. This release has 15.31 trillion bases and 2.49 billion records. The current release has 231,982,592 traditional records containing 940,513,260,726 base pairs of sequence data. There are also 1,653,427,055 WGS records containing 13,888,187,863,722 base pairs of sequence data, 498,305,045 bulk-oriented TSA records containing 440,578,422,611 … Continue reading GenBank release 245.0 → (Source: NCBI Insights)
Source: NCBI Insights - August 26, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New GenBank Source Type: news

Gene filtering in NCBI Sequence Viewer
We are excited to announce new track display options for gene annotation tracks in the NCBI Genome Data Viewer genome browser and other instances of the NCBI Sequence Viewer! Now, you can simplify gene annotation tracks to show only the genes and transcripts that you care about most.  For instance, you can choose to hide … Continue reading Gene filtering in NCBI Sequence Viewer → (Source: NCBI Insights)
Source: NCBI Insights - August 20, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Genome Data Viewer (GDV) Sequence Viewer Source Type: news

Update on My NCBI log-in changes and the Password Retirement Wizard
As we announced previously, the way you log into your My NCBI account will change from your My NCBI username and password to a 3rd-party login. On June 22, we disabled the ability to create new My NCBI passwords and in July we launched the Password Retirement Wizard, which will activate when you login here … Continue reading Update on My NCBI log-in changes and the Password Retirement Wizard → (Source: NCBI Insights)
Source: NCBI Insights - August 19, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New My Bibliography My NCBI SciENcv Source Type: news

Announcing the RefSeq annotation of sheep ARS-UI_Ramb_v2.0!
The new reference assembly for sheep is now annotated! Assembly ARS-UI_Ramb_v2.0 is made of 142 scaffolds, a drop from 2,640 in the 2017 assembly Oar_rambouillet_v1.0. With a contig N50 of 43 Mb, ARS-UI_Ramb_v2.0 is 15 times more contiguous than the first assembly of the Rambouillet breed. Annotation Release 104 (AR 104) of ARS-UI_Ramb_v2.0 reflects these improvements. Nearly 200 … Continue reading Announcing the RefSeq annotation of sheep ARS-UI_Ramb_v2.0! → (Source: NCBI Insights)
Source: NCBI Insights - August 12, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets Genome Genome annotation Genome assemblies Genome Data Viewer (GDV) NCBI Genome Remapping Service (NCBI Remap) RefSeq Source Type: news

Biosystems retiring March 2022 — use PubChem Pathways
The NCBI BioSystems Database will be retired in March 2022. This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content. NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource that offers a fresh, extended, and more modern interface. See the … Continue reading Biosystems retiring March 2022 — use PubChem Pathways → (Source: NCBI Insights)
Source: NCBI Insights - August 10, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New PubChem Source Type: news

Biosystems retiring in March 22 — use PubChem Pathways
The NCBI BioSystems Database  will be retired in March 2022. This retirement includes the representation of BioSystems records in the NCBI Entrez system and viewers of BioSystems content. NCBI now provides metabolic pathway and other biosystems data through the regularly updated PubChem Pathways resource that offers a fresh, extended, and more modern interface. See the … Continue reading Biosystems retiring in March 22 — use PubChem Pathways → (Source: NCBI Insights)
Source: NCBI Insights - August 10, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New PubChem Source Type: news

Search the NCBI Hidden Markov models collection against your favorite prokaryotic proteins
The NCBI Hidden Markov models (HMM) 6.0 release, available on our FTP site, has 15,247 models supported at NCBI. We created 80 more new HMMs and consolidated the collection by removing 2,151 HMMs that were nearly identical to another. Release 6.0 also incorporates 12,656 PFAM from release 34 that apply to prokaryotic proteins. You can … Continue reading Search the NCBI Hidden Markov models collection against your favorite prokaryotic proteins → (Source: NCBI Insights)
Source: NCBI Insights - August 10, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Hidden Markov Models (HMM) HMMER NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Source Type: news

Tackling Petabyte Scale Sequence Search Challenges
The volume of biological data being generated by the scientific community is growing exponentially, reflecting technological advances and research activities. This increase in available data has great promise for pushing scientific discovery but also introduces new challenges that scientific communities need to address. The National Institutes of Health’s (NIH) Sequence Read Archive (SRA), which is … Continue reading Tackling Petabyte Scale Sequence Search Challenges → (Source: NCBI Insights)
Source: NCBI Insights - August 9, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Sequence Read Archive (SRA) STRIDES Source Type: news

Aug 18 Webinar: Finding Data for your Research Organism: Plants and RNA-Seq data
Join us on August 18, 2021 at 12PM eastern time for the second webinar on finding data for your non-model research organism. In this webinar, you will learn how to use NCBI’s web resources to get data for a plant species, the black cottonwood. You will see how to find, access, and analyze gene and … Continue reading Aug 18 Webinar: Finding Data for your Research Organism: Plants and RNA-Seq data → (Source: NCBI Insights)
Source: NCBI Insights - August 6, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Datasets Gene expression Genome assemblies RNA-Seq Sequence Read Archive (SRA) SRA Toolkit Webinars Source Type: news

NCBI events at the Bioinformatics Open Science Conference 2021 (BOSC 2021)
Come visit us virtually to learn about new NCBI data access, tools and best practices at the Bioinformatics Open Science Conference  part of the ISMB/ECCB online conference from July 29 – 30, 2021. We will be presenting virtual posters on NCBI resources, offering a Birds of a Feather discussion, and participating in the BOSC  (CoFest) … Continue reading NCBI events at the Bioinformatics Open Science Conference 2021 (BOSC 2021) → (Source: NCBI Insights)
Source: NCBI Insights - July 27, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) BOSC2021 Cloud computing Conferences Datasets ElasticBLAST Magic-BLAST Sequence Read Archive (SRA) Source Type: news

Try out ElasticBLAST at the BOSC2021 CoFest!
Join the BLAST team at the virtual CollaborationFest (July 31 -August 1, 2021) after the BOSC 2021 conference to help test and improve ElasticBLAST, a new cloud-based tool designed to speed up high throughput BLAST searches. We would love to have your help with real world testing of our alpha release of ElasticBLAST with you … Continue reading Try out ElasticBLAST at the BOSC2021 CoFest! → (Source: NCBI Insights)
Source: NCBI Insights - July 27, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) BOSC2021 Cloud computing Conferences ElasticBLAST Source Type: news

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