Tag: NCBI Pathogen Detection

Full-scale access to microbial Pathogen Detection data in the Cloud!

Full-scale access to microbial Pathogen Detection data in the Cloud!

NCBI’s Pathogen Detection resource now provides selected data on the Google Cloud Platform (GCP) allowing you better access to over 1 million bacterial isolates.

Data on GCP include:

  1. The tables from the MicroBIGG-E database of anti-microbial resistance (AMR), stress response, virulence genes, and genomic elements and the Pathogen Isolates Browser that are both accessible through Google BigQuery.
  2. The MicroBIGG-E sequences in FASTA format that are available from Google Cloud Storage.

Features & Benefits

Pathogen Detection data on GCP allows you larger-scale access than is currently available through the web or from FTP.  Notably, there is no FTP access to MicroBIGG-E; the web interface is limited to 100K rows and sequence downloads are restricted.  There are no such restrictions on GCP. MicroBIGG-E at BigQuery also allows you to download all AMRFinderPlus results. Currently there are more than 20 million rows of antimicrobial resistance, virulence, and stress response genes, and point mutations, identified in more than 1 million pathogen isolates.

Here are two examples where researchers have used MicroBIGG-E and AMFinderPlus data to advance research on antimicrobial resistance:

    • Identifying conserved functional regions in erythromycin resistance methyltransferases (PMID: 34795028).
    • Assessing the health risks of antibiotic resistance genes (PMCID: PMC8346589).

Continue reading “Full-scale access to microbial Pathogen Detection data in the Cloud!” →

NCBI Workshop at the ASM NGS 2022 Meeting

NCBI Workshop at the ASM NGS 2022 Meeting

NCBI Microbial Pathogen and SARS-CoV-2 Resources in the Cloud

Get hands-on experience with NCBI Pathogen Detection and SARS-CoV-2 Surveillance data in the cloud. No prior cloud experience necessary!

NCBI staff are presenting a workshop at the American Society for Microbiology Next-Generation Sequencing (ASM NGS) 2022 Meeting on Sunday, October 16, 2022 from 10 am – 3 pm ET (with a 1 hour break) to help conference attendees learn about two NCBI cloud-hosted resources, Pathogen Detection and SARS-CoV-2 Genome Sequence datasets. Continue reading “NCBI Workshop at the ASM NGS 2022 Meeting” →

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 Campylobacter, E. 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” →