Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon Highlights
The National Institutes of Health (NIH) Office of Data Science Strategy (ODSS), the National Library of Medicine’s (NLM’s) National Center for Biotechnology and Information (NCBI), and the Department of Energy’s (DOE’s) Office of Biological and Environmental Research (BER) hosted scientists from around the world for a virtual Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon. The codeathon, … Continue reading Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon Highlights → (Source: NCBI Insights)
Source: NCBI Insights - December 17, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Basic Local Alignment Search Tool (BLAST) Codeathon Sequence Read Archive (SRA) Source Type: news
New annotations in RefSeq
In October and November, the NCBI Eukaryotic Genome Annotation Pipeline released twenty-nine new annotations in RefSeq for the following organisms: Acropora millepora (stony coral) Bubalus bubalis (water buffalo) Bufo gargarizans (Asiatic toad) Chrysoperla carnea (insect) (pictured) Coccinella septempunctata (seven-spotted ladybird) Coregonus clupeaformis (lake whitefish) Cotesia glomerata (wasp) Daphnia magna (crustacean) Desmodus rotundus (common vampire bat) Drosophila ananassae (fly) Drosophila … Continue reading New annotations in RefSeq → (Source: NCBI Insights)
Source: NCBI Insights - December 15, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New Eukaryotic genome annotation RefSeq Source Type: news
Save the Date: NCBI at Plant and Animal Genome (PAGXXIX), Jan 2022
Come see NCBI in person at the International Plant and Animal Genome (PAG) Conference (PAGXXIX), January 9-12 in San Diego, California. Learn about new ways that we are supporting the data management and analysis needs of scientists working across the tree of life. We’re excited to be back after a year of unprecedented circumstances! As … Continue reading Save the Date: NCBI at Plant and Animal Genome (PAGXXIX), Jan 2022 → (Source: NCBI Insights)
Source: NCBI Insights - December 10, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New CGR Conferences Eukaryotic genome annotation PAGXXIX Source Type: news
NCBI Taxonomy to include phylum rank in taxonomic names
NCBI Taxonomy will append a list of 42 names of prokaryote phyla published for validation purposes as required under the International Code of Nomenclature for Prokaryotes (ICNP). You can still search for previous informal names, and any informal phylum rank names not addressed in the validation list will remain unchanged. The largest named groups affected … Continue reading NCBI Taxonomy to include phylum rank in taxonomic names → (Source: NCBI Insights)
Source: NCBI Insights - December 10, 2021 Category: Databases & Libraries Authors: NCBI Staff Tags: What's New NCBI Taxonomy Source Type: news
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
