Relevant NCBI Resources

A Collection of NCBI resources that have been requested by codeathon teams or can be beneficial for teams during the event. 

Key resources:

• NCBI Pathogen Resources: this list provides a broader overview of NCBI resources relevant to pathogen research, including databases, tools, and software specifically designed for studying pathogens and is a valuable starting point.
• National Database of Antibiotic Resistant Organisms (NDARO): centralized hub provides access to antimicrobial resistance (AMR) data for real-time surveillance of pathogenic organisms.
• Isolates Browser: explore metadata associated with bacterial and fungal isolates.
• MicroBIGG-E: analyze bacterial genomes for biosynthetic potential, including antibiotic resistance genes.
• Antibiotic Susceptibility Test (AST) Browser: search for antibiotic resistance data from various sources.
• NCBI Pathogen Detection Resources at Google Cloud Platform

Databases:

1. GenBank: Comprehensive collection of publicly available DNA sequences and supporting information.
2. SRA: Archive of raw sequencing data from various sequencing platforms.
3. BioSample: Collection of descriptions of biological samples used in experimental studies.
4. PubMed: Database of biomedical literature citations and abstracts.
5. PMC: Full-text archive of biomedical and life sciences journal articles.
6. ClinVar: Archive of reports of the relationships between human variations and phenotypes.
7. dbGaP: Archive of datasets from studies that have investigated the interaction of genotypes and phenotypes.
8. GEO: Public repository for high-throughput gene expression and other functional genomics data.
9. PubChem: Database of chemical structures and biological activities.
10. Structure: Archive of 3D biomolecular structures.
11. Protein: Resource for protein sequence and functional information.
12. Genome: Resource for whole genome sequencing data.
13. GTEx: Database of gene expression and regulation across human tissues.
14. dbSNP: Database of human single nucleotide polymorphisms (SNPs).
15. OMIM: Catalogue of human genes and genetic disorders.

Tools:

1. BLAST for comparing biological sequences.
2. Gene for accessing and analyzing gene-specific information.
3. Entrez search and retrieval system for NCBI databases.
4. iCn3D for interactively visualizing and analyzing 3D protein structures.