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NCBI INSIGHTS

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NCBI INSIGHTS ARCHIVES

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ENHANCEMENTS TO CLINVAR WEBSITE NOW LIVE

As previously announced, we updated the ClinVar website as part of our effort to
better support the display of submitted somatic variation data. 

WHAT CHANGED? 

Continue reading “Enhancements to ClinVar Website Now Live” →

 * NCBI Staff
 * January 31, 2024

 * ClinVar


HOMOLOGENE NOW REDIRECTS TO NCBI DATASETS GENE


A NEW WAY TO VIEW AND DOWNLOAD RELATED GENES 

As previously announced, HomoloGene now automatically redirects to the NCBI
Datasets Gene page giving you easy access to up-to-date sequence and homology
data. The NCBI Datasets Gene Table provides a link to NCBI Orthologs with
expanded gene and protein information and links to tools. NCBI Orthologs
includes more genes and sequences for a growing range of taxa. See an example
below. Legacy HomoloGene data remains available on the FTP site. Continue
reading “HomoloGene Now Redirects to NCBI Datasets Gene” →

 * NCBI Staff
 * January 30, 2024

 * Comparative Genomics Resource (CGR)
 * Gene
 * Homologs
 * NCBI Datasets


BLAST FASTA FILES WILL NO LONGER BE AVAILABLE ON THE FTP SITE EFFECTIVE APRIL
2024


EASILY GENERATE BLAST FASTA FILES YOURSELF! 

In April 2024, the FASTA (sequence text) files of the sequences in the Basic
Alignment Search Tool (BLAST) databases will no longer be available on the FTP
site. However, you can easily generate FASTA files yourself from the formatted
BLAST databases by using the BLAST utility blastdbcmd that comes with the
standalone BLAST programs. This provides you the flexibility to generate
organism-specific FASTA files using NCBI’s taxonomy IDs for specific organisms
or groups.   

See the examples below and the BLAST Command Line Applications User Manual for
more details on the standalone BLAST programs and working with the BLAST
databases.  Continue reading “BLAST FASTA Files Will No Longer Be Available on
the FTP Site Effective April 2024” →

 * NCBI Staff
 * January 25, 2024

 * Basic Local Alignment Search Tool (BLAST)
 * FASTA
 * NCBI Taxonomy


UPDATED BACTERIAL AND ARCHAEAL REFERENCE GENOME COLLECTION IS AVAILABLE!

Download the updated bacterial and archaeal reference genome collection! This
collection (18,941 genomes as of Jan 18, 2024) was built by selecting the “best”
genome assembly for each species among the 330,000+ prokaryotic genomes in
RefSeq (except for E. coli for which two assemblies were selected as reference).
You can speed up your sequence searches by running them against these
high-quality genomes instead of the entire nucleotide or protein database.

The criteria for selecting the reference assembly for a given species include
assembly contiguity and completeness and quality of the RefSeq annotation.
Continue reading “Updated Bacterial and Archaeal Reference Genome Collection is
Available!” →

 * NCBI Staff
 * January 18, 2024January 18, 2024

 * Basic Local Alignment Search Tool (BLAST)
 * NCBI Taxonomy
 * Nucleotide BLAST (blastn)
 * Prokaryotic genome annotation
 * RefSeq


REFSEQ RELEASE 222 NOW AVAILABLE!

Check out RefSeq release 222, now available online and from the FTP site. You
can access RefSeq data through NCBI Datasets.

WHAT’S INCLUDED IN THIS RELEASE?

As of January 8, 2024, this full release incorporates genomic, transcript, and
protein data containing:

 * 411,137,832 records
 * 304,562,770 proteins
 * 59,343,570 RNAs
 * sequences from 145,371 organisms 

Continue reading “RefSeq Release 222 Now Available!” →

 * NCBI Staff
 * January 16, 2024January 17, 2024

 * Comparative Genomics Resource (CGR)
 * NCBI Datasets
 * RefSeq


NOW AVAILABLE: NCBI HIDDEN MARKOV MODELS (HMM) RELEASE 14.0!

Download release 14.0 of the NCBI protein profile Hidden Markov models (HMMs)
used by the Prokaryotic Genome Annotation Pipeline (PGAP)! Search this
collection against your favorite prokaryotic proteins to identify their function
using the HMMER sequence analysis package. Continue reading “Now Available: NCBI
Hidden Markov Models (HMM) Release 14.0!” →

 * NCBI Staff
 * January 11, 2024

 * Hidden Markov Models (HMM)
 * HMMER
 * NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
 * RefSeq


BEST OF 2023: A LOOK AT THE NCBI INSIGHTS BLOG

As we begin a new year, let’s look back at the best NCBI Insights Blog posts of
2023.  

In case you missed any of these, check them out!  Continue reading “Best of
2023: A Look at the NCBI Insights Blog” →

 * NCBI Staff
 * January 4, 2024




GENBANK RELEASE 259.0 IS AVAILABLE!

GenBank release 259.0 (12/22/2023) is now available on the NCBI FTP site. This
release has 27.94 trillion bases and 3.96 billion records.

The current release has:

 * 247,777,761 traditional records containing 2,433,391,164,875 base pairs of
   sequence data
 * 2,775,205,599 WGS records containing 23,600,199,887,231 base pairs of
   sequence data
 * 701,336,089 bulk-oriented TSA records containing 659,924,904,311 base pairs
   of sequence data
 * 130,654,568 bulk-oriented TLS records containing 50,868,407,906 base pairs of
   sequence data

Continue reading “GenBank Release 259.0 is Available!” →

 * NCBI Staff
 * December 28, 2023December 28, 2023

 * GenBank


USING NCBI DATA AND TOOLS FOR YOUR RESEARCH PROJECT

Are you a biology student working on a research project? NCBI offers free access
to a wide variety of resources and tools to help you find and download data for
your project.  

HOW AND WHY DO YOU USE OUR RESOURCES? CHECK OUT THE EXAMPLE BELOW:

Your professor has assigned you a research project looking at the sequence and
structure of the TP53 gene in the domestic cat (Felis catus). In addition, you
were asked to find information on this gene and its genomic region in other
members of the cat family (Felidae).  Continue reading “Using NCBI Data and
Tools for Your Research Project” →

 * NCBI Staff
 * December 18, 2023January 23, 2024

 * Basic Local Alignment Search Tool (BLAST)
 * Comparative Genome Viewer (CGV)
 * Comparative Genomics Resource (CGR)
 * Gene
 * Genome
 * Genome Data Viewer (GDV)
 * iCn3D
 * NCBI Datasets
 * NCBI Taxonomy
 * PubMed Central (PMC)


UPDATE TO GENBANK QUALIFIER

‘COUNTRY’ WILL TRANSITION TO ‘GEOGRAPHIC LOCATION’ EFFECTIVE JUNE 2024

As announced earlier this year, we will begin to systematically gather ‘location
of collection’ and ‘date and time of collection’ for sequence data submitted
to GenBank and the Sequence Read Archive (SRA).

As part of this effort and to make location data more accurate and informative,
we are also changing the way this information is represented on GenBank records,
consistent with the relevant field in BioSample. Continue reading “Update to
GenBank Qualifier” →

 * NCBI Staff
 * December 14, 2023

 * GenBank
 * Sequence Read Archive (SRA)


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