Fungal species identification using DNA: a NCBI and USDA-APHIS collaboration with a focus on Colletotrichum

As reported in the journal Plant Disease,  a recent collaboration between National Library of Medicine’s NCBI and the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (APHIS) analyzed public sequence records for the fungal genus Colletotrichum, an important group of fungal plant pathogens that are a significant threat  to food production. Colletotrichum species … Continue reading Fungal species identification using DNA: a NCBI and USDA-APHIS collaboration with a focus on Colletotrichum

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ASM Microbe 2022 was a success!

NCBI had the pleasure of attending and participating in this year’s American Society of Microbiology (ASM) Microbe conference, June 9-13 in Washington, D.C. NCBI staff participated in activities and events throughout the three-day conference. Over 4,500 attendees gathered in the exhibit hall and joined a variety of poster presentations and talks! Reflections from a few … Continue reading ASM Microbe 2022 was a success!

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PubMed API launch is pushed back

As we previously announced, we will be moving to an updated version of the E-utilities API for PubMed. In preparation for this launch, a test server is currently available to allow you to test your API calls on the new service and report issues. Thank you for trying out the test server and continuing to … Continue reading PubMed API launch is pushed back

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Announcing an updated prokaryotic representative genomes collection with 706 new species!

An updated bacterial and archaeal representative genomes collection is available! A total of 16,105 assemblies among the 249,000 prokaryotic assemblies in RefSeq were selected to represent their respective species. The collection has grown by 3.7% since January 2022. A total of 706 species are represented for the first time. In addition, 186 species are represented … Continue reading Announcing an updated prokaryotic representative genomes collection with 706 new species!

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Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022

Come visit NCBI at the Bioinformatics Open Science Conference (BOSC), part of the Intelligent Systems for Molecular Biology Conference (ISMB), July 13-16, taking place both in person in Madison, Wisconsin and virtually! We’ll be presenting talks and posters on the latest updates to the NCBI Datasets, BLAST, and Protein resources. You can also join us at … Continue reading Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022

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June 15 Webinar: What’s new with NCBI Virus?

Join us on June 15 , 2022 at 12PM US eastern time learn about the NCBI Virus resource – a community portal for viral sequence data that has been important in supporting SARS-CoV-2 research and management of the COVID-19 pandemic. Enhancements to NCBI Virus that support these efforts include: SARS-CoV-2 specific filters, a dedicated web … Continue reading June 15 Webinar: What’s new with NCBI Virus?

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Come see NCBI at the ASM Microbe Conference 2022

The American Society of Microbiology (ASM) Microbe conference is back, and scheduled to take place in-person, June 9th-13th in Washington, D.C. NCBI staff member Dr. Michael Feldgarden will be recognized by ASM with an award for his research. Other NCBI staff will present posters on NCBI resources and will also be available at our booth … Continue reading Come see NCBI at the ASM Microbe Conference 2022

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Average Nucleotide Identity (ANI) for assembly validation

Validating genome assemblies submitted to GenBank using ANI based workflow Average Nucleotide Identity (ANI) analysis is a useful tool to verify taxonomic identities in prokaryotic genomes. As part of the NCBI bacterial genome submission process, GenBank performs ANI analyses to compare submitted prokaryotic genome assemblies against reference data generated from type strains. You can learn … Continue reading Average Nucleotide Identity (ANI) for assembly validation

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Monkeypox virus: Complete genome from the current outbreak now available in GenBank

The first complete genome sequence of the current monkeypox virus (MPXV) outbreak (isolate name MPXV_USA_2022_MA001) is now available with accession ON563414 in GenBank, a public database of DNA sequences hosted by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). Several cases of monkeypox have been identified in geographically widespread … Continue reading Monkeypox virus: Complete genome from the current outbreak now available in GenBank

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New in RAPT: Better taxonomic assignment and GO annotation

We are excited to announce two improvements to the Read assembly and Annotation Pipeline Tool (RAPT), which allows you to assemble genomic reads for bacterial or archaeal isolates and annotate their genes at the click of a button. Improved taxonomic assignment Now RAPT verifies the scientific name you provide with the reads, and corrects it … Continue reading New in RAPT: Better taxonomic assignment and GO annotation

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