Antimicrobial Resistance Resources

Housed within the NCBI Pathogen resource, the NCBI National Database of Antibiotic Resistant Organisms (NDARO) provides access to antimicrobial resistance (AMR) data to facilitate real-time surveillance of pathogenic organisms and tools such as AMRFinderPlus for analysis of microbial genomes.

BLAST

BLAST® finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

Microorganism Classification Identification (MiCId)

The Microorganism Classification Identification (MiCId) workflow can perform microorganismal identifications, protein identifications, sample biomass estimates, and antibiotic resistance protein identifications in 6-15 minutes per MS/MS sample using computing resources. MiCId’s workflow is fast, portable, and with high sensitivity and high precision, making it a valuable tool for rapid identifications of bacteria as well as detection of their antibiotic resistance proteins. MiCId workflow is freely available for download!

Foreign Contamination Screen (FCS)

The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.

NCBI Datasets

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases in the website or with command-line tools or APIs. Find and download gene, transcript, protein and genome sequences, annotation and metadata.

Prokaryotic Genome Annotation Pipeline (PGAP)

A tool developed to annotate bacterial and archaeal genome sequences (chromosomes and plasmids) for submission to NCBI. In addition to use during submission in a web form, PGAP is also available as a stand-alone software package that you can run yourself to produce annotated genomes ready for submission to GenBank.

Taxonomy

The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

GenBank

GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis.

The NCBI Submission Portal

NCBI's Submission Portal allows you to submit your data to the world's largest public repository of biological and scientific information.

RefSeq

The NCBI Reference Sequence Database (RefSeq) is a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

Sequence Read Archive (SRA)

Sequence Read Archive data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information (if submitted) to enhance reproducibility and facilitate new discoveries through data analysis.

PubMed

PubMed® comprises more than 34 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

PubMed Central (PMC)

PubMed Central® (PMC) is a free full-text archive of biomedical and life sciences journal literature.