Tag: NCBI Pathogen Detection

ASM Microbe 2022 was a success!

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 of our NCBI experts

“It was a great honor for me to receive the ASM Elizabeth O. King Lecturer Award. Thank you to my colleagues, without whom so much of my work would not have been possible, and to all of those who attended my presentation on Making Genomics Accessible to Aid Public Health and Research.”

~Michael Feldgarden, Ph.D.  Continue reading “ASM Microbe 2022 was a success!”

Come see NCBI at the ASM Microbe Conference 2022

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 (#1128) to address your questions. Drop by to see what’s new and provide your feedback. We hope to see you there! Check out NCBI’s schedule of activities:  Continue reading “Come see NCBI at the ASM Microbe Conference 2022”

Assembly database passes 1 million genome assemblies!

The NCBI Assembly database now provides sequence and metadata for more than 1 million genome assemblies from over 85,000 different species.

Assembly crossed the 1 million genome assemblies milestone on Sunday, April 18, 2021 (Figure 1).

Figure 1. Assembly status and growth. More than 1 million assemblies are now searchable through the NCBI web site (top panel). The number of genome assemblies at NCBI has accelerated rapidly in the past decade.

Continue reading “Assembly database passes 1 million genome assemblies!”

Search NCBI’s Pathogen Detection websites with simple keywords

We’ve redesigned the filters on NCBI’s Pathogen Detection websites to make searching easier!

For example, say you wanted to search for outbreak isolates related to flour. Before the filters were redesigned, you’d have to know that some of the available metadata terms include “flour”, “All-purpose Wheat flour”, and “wheat flour”, along with seventeen other terms. Now, you can see all of your available options after typing in your search term and select only those that are relevant to your search.

Figure 1. Isolates Browser. The “Filters” button to see and search all filters.

Continue reading “Search NCBI’s Pathogen Detection websites with simple keywords”

New publication on AMRFinder, a tool that identifies resistance genes in pathogen genomes!

Read the recent publication (PMID: 31427293) on the AMRFinder, a tool that identifies antimicrobial resistance (AMR) genes in bacterial genome sequences using a high-quality curated AMR gene reference database.  We use the AMRFinder to identify AMR genes in the hundreds of bacterial genomes that NCBI receives every day, and the results of AMRFinder are used in NCBI’s Isolates Browser to provide accurate assessments of AMR gene content. You can install AMRFinder locally and run it yourself. Follow the instructions on our GitHub site.

Since the publication we have upgraded AMRFinder to AMRFinderPlus. The enhanced tool now

  • supports searches based on protein annotations, nucleotide sequences, or both for best results
  • identifies point mutations in CampylobacterE. coli, Shigella, and Salmonella
  • optionally identifies many genes involved in biocide, heat, metal, and stress resistance, as well as many antigenicity and virulence genes
  • provides information about gene function, including resistance to individual antibiotics and other phenotypes

You can learn more about NCBI’s role in helping to combat antimicrobial resistance at the National Database of Antibiotic Resistant Organisms.

May 15, 2019 Webinar: Using taxonomic information and other improvements in standalone BLAST+ (2.9.0) and the v5 databases

May 15, 2019 Webinar: Using taxonomic information and other improvements in standalone BLAST+ (2.9.0) and the v5 databases

Next Wednesday, May 15, 2019 at 11AM, NCBI staff will show you how to use the latest version of standalone BLAST+ (2.9.0) and the new accession-based DBv5 databases with built-in taxonomy information. You will learn how to limit searches to taxonomic groups and to retrieve sequences from the database by taxonomy without having to download an identifier list. You will also learn about additional improvements in the BLAST databases and programs that make them compatible with the new PDB identifiers and gi-less proteins from the Pathogen Detection Project.

Date and time: Wed, May 15, 2018 11:00 AM – 11:30 AM EDT

Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Recent enhancements to BLAST+ (2.9.0): built-in taxonomy and access to proteins from the Pathogen Detection Project

We have made some recent improvements to the BLAST+ applications that take full advantage of the version 5 BLAST databases (BLASTDBv5), which include built in taxonomic information for sequences and no longer rely on the integer sequence identifiers (gi numbers).

With the latest version of BLAST, you can now:

Continue reading “Recent enhancements to BLAST+ (2.9.0): built-in taxonomy and access to proteins from the Pathogen Detection Project”

Track pathogenic organisms promptly with the National Database of Antibiotic Resistant Organisms

In response to the rising threat of antimicrobial resistance (AMR), NCBI built the National Database of Antibiotic Resistant Organisms (NDARO). With NDARO, you can:

FIG 1
Figure 1. Filter your Isolates Browser results based on date, location, and for antibiotic resistance (whether the isolate has any AMR genes, or any Antimicrobial Susceptibility Testing (AST) phenotype submitted).

Continue reading “Track pathogenic organisms promptly with the National Database of Antibiotic Resistant Organisms”

NCBI releases enhanced Pathogen Detection (Beta) Isolates Browser

NCBI has introduced a new and improved Pathogen DetectionBeta Isolates Browser. The browser is a key component of NCBI’s Pathogen Detection Project, a collaboration with FDA, CDC, USDA, and others to use whole genome sequencing data to monitor and investigate outbreaks of foodborne disease. Federal, state and other labs sequence pathogens (such as Salmonella and Listeria) isolated from patients, food, and environmental samples and submit the data in real time to NCBI. We then use our analysis pipeline to assemble the sequences and cluster them with all other isolates in the database to identify closely related sequences, thereby making it easier to identify cases that could be involved in an outbreak.

What’s new?

The browser is a completely updated interface that offers many improvements, like:

  • An enhanced search and browse interface
  • A new tree viewer that allows easy navigation of large SNP clusters

The NCBI Pathogen DetectionBeta home page allows direct access to sequence data, submission resources, and documentation.

Continue reading “NCBI releases enhanced Pathogen Detection (Beta) Isolates Browser”