With the Comparative Genome Viewer you can compare two assemblies to see differences in genomic sequence and structure. Check out our new visualization tool! ow.ly/6aTK50K4S7W #NCBICGR
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Get rapid access to #Wuhan #coronavirus sequence data and analytics. Newly-released GenBank data available here: go.usa.gov/xdjvv
NCBI Hidden Markov Models (HMM) Release 13.0 is now available! This release has 16,143 HMMs and 315 new HMMs since release 12.0. Learn more:
RefSeq prokaryotic genomes and proteins are now annotated with Gene Ontology (GO) terms! Learn more: loom.ly/39YAUuM
Get rapid access to #Wuhan #coronavirus sequence data from the current outbreak as it becomes available. We will continue to update the page with newly released data. go.usa.gov/xd2Mc
NCBI will use ANI analysis to correct existing public records in GenBank. This will ensure that taxonomic information on genome assemblies is as accurate as possible.
The latest post on NCBI Insights explains how we’ll correct these records.
Introducing the Comparative Genome Viewer (CGV)! The CGV is an easy-to-use visualization tool that helps you quickly compare eukaryotic genome assemblies and identify genomic changes that may be significant to biology and evolution. Learn more:
ow.ly/ZiXt50JOK5i #NCBICGR
The new Comparative Genome Viewer can help you easily identify genomic changes that may be significant to biology and evolution. Try it out and let us know what you think! Learn more about the visualization tool here: ow.ly/a7iZ50K4SNC #NCBICGR
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Happy #DNADay2023! Join us in celebrating the 20th anniversary of the Human Genome Project’s completion and the 70th anniversary of the discovery of the DNA double helix. Learn all about DNA Day: genome.gov/dna-day/about
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BLAST+ 2.8.1 is released with new databases and better performance
The first complete sequence of a human genome, known as T2T-CHM13, is now available! Finding the new assembly at NCBI is easy. More info here:
ow.ly/ahp750Jcpi4
The first complete genome sequence of the current monkeypox virus outbreak is now available in GenBank. Learn more:
#COVID19 is an emerging, rapidly evolving situation. Learn about the basics like symptoms & what to do if you are sick; and see the latest info from on #NIH’s page: nih.gov/health-informa #coronavirus
BLAST+ 2.13.0 now available with SRA BLAST, ARM Linux executables, and database metadata! loom.ly/5TCdIFo #NCBIBLAST
We are happy to announce a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP)! Learn about the new features and updates here: loom.ly/R_mSI88
#NCBIBLAST+ 2.14.0 now with faster protein and translated searches. You can search nr over 20% more quickly and smaller databases up to 3 times faster. More details 👉ow.ly/gOkk50Oh1eJ
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GenBank Release 248.0 is now available! This release has 17.11 trillion bases and 2.62 billion records. Since the last release, 52,784 records were updated. Learn more: loom.ly/6Lj6DLU
The latest version of the BLAST databases lets you:
1. Limit your search by taxonomy using information built into the BLAST databases
2. Search sequences by accession faster
3. Use blastdbcmd to retrieve sequences by taxonomy from a BLAST database
#bioinformatics
We are excited to announce a new feature in the Multiple Sequence Alignment (MSA) Viewer! You can now search the anchor or consensus sequence of a multiple alignment for short sequence strings. Learn more here: loom.ly/ChhALLE
NCBI hidden Markov models (HMM) release 4.0 now available! This release contains 17,443 models, including 94 new models since the last release. Read more: ncbiinsights.ncbi.nlm.nih.gov/2020/12/21/ncb
Primer-BLAST can now design primers for a group of related target sequences!
ow.ly/JFaA50BBITS
APPLY NOW for our virtual workshop, “An Update on NCBI #BLAST and Other Sequence Analysis Tools”! #SciEd #Bioinformatics
#NCBIBLAST+ 2.14.1 now available with improved documentation, faster and more reliable database downloads, and some bug fixes. More info and download: blast.ncbi.nlm.nih.gov/doc/blast-news
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NIH’s Sequence Read Archive (SRA) will be freely accessible through Amazon's Open Data Sponsorship Program! Read more:
Announcing the SARS-CoV-2 Variant Calling Pipeline! This new analysis pipeline can uniformly process raw sequence data produced by various sequencing platforms. Learn more 👉 ow.ly/UAB250LSTaa
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A new version of the Prokaryotic Genome Annotation Pipeline (PGAP) is available! This release includes structural and functional annotation improvements and bug fixes. Learn more: loom.ly/D06MKG4
New to finding NCBI #data? Join our workshop, An Introduction to Pathogen Data at NCBI, to learn how to best access #microbial & #pathogen data! More info here 👇
loom.ly/zAMpBYw
#SciEd #BioInformatics
The #BLAST #Docker and databases are now ready to use on Google and Amazon clouds #CloudComputing
ow.ly/uPCB50Asgez
You asked, we listened! We are pleased to announce that you can now search for a gene in our Comparative Genome Viewer (CGV) and navigate directly to its location in the viewer. Learn more 👉ow.ly/CL7x50M2g90 #NCBICGR
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#SARS-CoV-2 sequence data is essential in the fight against the #COVID19 pandemic. Submit your sequence data to the INSDC (GenBank , ENA , and DDBJ ) to support and maintain rapid #OpenAcess to these crucial data ow.ly/UGiH50B1wYb
NCBI Pathogen Detection now contains over one million isolate genomes from 48 organism groups: 47 bacterial, and one fungal!
loom.ly/aCdU0ys
You can now retrieve #genome data by #BioProject with the #Datasets command-line tool!
loom.ly/Apl8qdM
We have updated the Prokaryotic representative genome collection, which includes over 900 new species! Learn more: loom.ly/Nu1IXPw
Wow! Thanks! We'll keep working to make sure that BLAST is a useful, powerful, essential bioinformatics tool.
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Coming soon! Beginning in the first week of January 2023, NCBI Taxonomy will initiate changes to prokaryote phylum names. Learn more: ow.ly/oPNr50LCLov
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Apply to our virtual workshop, "Using NCBI’s Primer-BLAST to Design & Analyze PCR Primers" by May 23rd! Learn more here: loom.ly/xwexYbY
#SciEd #BLAST #Bioinformatics #PrimerDesign
Now available! HMM Release 11.0 contains 15,643 models. Learn more 👉
💻 New #Codeathon Opportunity! We are teaming up with the National Institute of Allergy and Infectious Diseases to host a Beyond Phylogenies Visualizations Codeathon. Apply today! 👇
loom.ly/sBxKaqo
#Bioinformatics #CodingLife #Networking
We reannotated over 1,000 Streptomyces genomes! Read more on NCBI Insights: go.usa.gov/xQtpX
Prokaryotic Genome Annotation Pipeline (PGAP) now produces files suitable for submission to GenBank!
Release 12.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available! Check out what's new 👇
The new #SRA Lite format from the Sequence Read Archive slims down your data reducing the average read size by ~60% for more efficient analysis and storage of large next-gen datasets! loom.ly/GbhoTUs
📣 Last chance to apply for our #virtual workshop, An Introduction to Pathogen Data at NCBI. Learn how to access #microbial & #pathogen data!
loom.ly/zAMpBYw
#SciEd #BioInformatics
The updated NCBI Datasets Genomes page now has genome data for all domains of life, including bacterial and viral genomes! Check out the new filters and actions available in the genomes table: loom.ly/JC-iSV8
Need genomic sequence and annotation data for a eukaryotic organism? Now you can easily gather that data from across NCBI with Datasets! ncbi.nlm.nih.gov/datasets/
Read more about the new resource on NCBI Insights and give it a try today. ncbiinsights.ncbi.nlm.nih.gov/2020/03/30/ncb
New ribosomal RNA BLAST databases available on the web BLAST service and for download
Next week, NLM will launch a pilot project to test the viability of making preprints—scholarly manuscripts posted by the author(s) to openly accessible platforms, usually before peer review— resulting from NIH-funded research available via PubMed Central.
GenBank Release 253.0 is now available. Since the last release, we added one trillion bases and 150 million records! Learn more 👉
Applications are open for our virtual workshop, "Getting Started with NCBI Data in #Python"! Apply by Nov. 21st! loom.ly/Ny3WekI
#SciEd #Bioinformatics
We are making several improvements to our SRA database, the largest publicly available repository of high throughput sequencing data! Learn about the enhancements here 👉 ow.ly/NZmL50NcfFG #NCBISRA
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Did you know you can download and run the Prokaryotic Genome Annotation Pipeline on your own machine or in the cloud?
Give it a try and send us your thoughts!
Looking for genomes for SARS-CoV-2 variants? NCBI now supports searches for SARS-CoV-2 variant names such as B.1.1.7, B.1.351, or P.1. Learn more: loom.ly/nrA6aeA
Get the latest release of Magic-BLAST (1.6.0), NCBI's next-gen alignment tool. Now with usage reporting, access to SRA in the cloud, taxids in SAM output, file upload of SRA accessions and more! ow.ly/ljb650JLHgM #NCBIBLAST #NCBImagicBLAST
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RefSeq Release 212 is available and contains the first new annotation of human in four years! It also contains new annotations for 29 species, including: gray squirrel, American grasshopper, and fishing cat. Read more:
NEW PubMed proximity search feature! Combine a phrase search and a proximity search in the same query using Boolean operators, such as AND, OR, NOT. Here is an example: ow.ly/zJWF50MaTk0
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NCBI is now producing a new set of taxonomy files that include the taxonomic lineage of taxa, information on type strains and material, and host information.
There is still time to apply for our virtual workshop, "An Introduction to NCBI Cloud Computing for Biologists"! More info here 👇💻☁️
loom.ly/EXkCN60
#CloudComputing #SciEd #GradChat #Bioinformatics
Download NCBI's #Prokaryotic #GenomeAnnotation Pipeline (PGAP) and run it on your own machine, a compute farm, or in the #Cloud on your own data! loom.ly/Hp9xn7g
Do you want to learn how to use Primer-BLAST to design specific primers for PCR? Check out our upcoming workshop on September 26! Application deadline is September 12. More info: ow.ly/2Y3u50PAq0f #NCBIBLAST
The BLAST programs and databases are available in Docker and cloud-ready!
Get programmatic access to NCBI gene and sequence data through Datasets command-line tool and API!
ow.ly/szLu50C62XZ
Conserved Domain Database (CDD) version 3.20 is now live! Version 3.20 contains 1,614 new or updated NCBI/CDD-curated domains. Learn more here 🔗ow.ly/EHWy50KToOR
#NCBICGR #Bioinformatics
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Applications for our virtual workshop, "An Introduction to NCBI Cloud Computing for Biologists" are OPEN NOW! More info here 👇
loom.ly/EXkCN60
#CloudComputing #SciEd #GradChat #Bioinformatics
An updated bacterial and archaeal representative genomes collection is available! A total of 610 species are represented for the first time. Learn more 👇 ow.ly/yQbw50L7ouT
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We are updating influenza virus names to reflect changes to the International Code of Virus Classification and Nomenclature (ICVCN). Name changes will take effect this summer! Learn more 👉 ow.ly/ybUV50MYrsG
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New release of the Read Assembly and Annotation Pipeline Tool (RAPT), now 2X faster! loom.ly/YOxHOG4
All of the Sequence Read Archive (SRA) now live on two cloud platforms! ow.ly/r5KO50yuDdd
Ever gone virus hunting? If so, we need your help! Join us at the SoCal #Bioinformatics Hackathon! We’ll upload known & novel viruses from >100K datasets to the cloud. You’ll code and problem-solve to ID them.
Apply here (deadline - December 12 3pm PT):
A more modern PubMed Central (PMC) is coming - let us know what you think in PMC Labs! loom.ly/0T_12bw
An updated bacterial and archaeal reference genome collection is available! A total of 497 species are included in this collection for the first time and 174 species are represented by a better assembly. Learn more:
RefSeq release 82 contains the complete reannotation of prokaryotic genomes, including E.coli & salmonella go.usa.gov/xN23c
Test server for the PubMed API (E-utilities) is now available! We will be moving to an updated version of the E-utilities API for PubMed in June 2022. Don’t wait until launch! Try the test server and provide feedback. Learn more here: loom.ly/zuUJITE
Next month, we’ll be at for a pangenomics in the cloud #hackathon!
Apply today: goo.gl/forms/WCmWSV32
More info: go.usa.gov/xENgE
#bioinformatics
NCBI is making it easy to run BLAST on the cloud! #ElasticBLAST #CloudComputing #NCBIBLAST #BioIT22 ow.ly/eW3X50ITIxl
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RefSeq Release 210 is now available! This full release contains sequences from 115,929 organisms and new annotations for 26 species, including domestic ferret, cat, yellowpond turtle, swimming crab and domesticated barley. Learn more: loom.ly/0nTb154
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. Learn more here:
ncbiinsights.ncbi.nlm.nih.gov/2020/11/24/rea
Quickly compare eukaryotic genomes with our new Comparative Genome Viewer! Learn more about this easy-to-use visualization tool: ow.ly/wv2F50K1zVu #NCBICGR
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Read the new publication on AMRFinder, a tool that identifies resistance genes in pathogen genomes!
Did you know that RAPT produces RefSeq-quality annotated genomes? RAPT annotates the assembly it creates using PGAP - including the same expert-curated HMMs, domain architectures and more used to annotate RefSeq assemblies. Try RAPT here: loom.ly/p9MFzaI
PubMed will be moving to an updated version of the E-utilities API in November! Learn more:
#NCBI #BLAST Tip: Do you want to align next generation DNA- and RNA-Seq sequencing reads? Magic-BLAST version 1.5.0 is here to help! ow.ly/Qdn230qnPgO
Introducing ElasticBLAST – BLAST® is now easier, bigger, and faster on the Cloud! To learn more about ElasticBLAST, check out our introduction at loom.ly/4rc9crI
Learn more about using NCBI’s Primer-BLAST to design & analyze PCR primers in our virtual workshop (November 9th,1-2:30pm ET). Applications close October 15th. Learn more here: loom.ly/p3fueZ4 !
#SciEd #BLAST #Bioinformatics
Novel coronavirus complete genome from the Wuhan outbreak now available in GenBank! ncbiinsights.ncbi.nlm.nih.gov/2020/01/13/nov
Check out the latest Prokaryotic Genome Annotation Pipeline #PGAP release with Singularity, no-internet option, and Taxonomy Check ncbiinsights.ncbi.nlm.nih.gov/2020/02/20/new
PubMed is now available for download without a license and can be updated every day!
Join us for our virtual workshop, "Identifying Clinically Relevant Genes in Bacterial Genomes"! Applications are now open: loom.ly/HslnJaU #SciEd
The NCBI Assembly database now provides sequence and metadata for more than 1 million genome assemblies from over 85,000 different species! Learn more: loom.ly/gyqd_ZM
BLAST now offers RefSeq Select databases: smaller databases with high quality sequences!
ow.ly/sikR50BUZaN
