Biomedical Science

Bioinformatics Databases and NCBI Tools

NCBI Resources

What is NCBI

National Center for Biotechnology Information (NCBI)

NCBI logo

The National Center for Biotechnology Information (NCBI) advances science and health by providing access to genomic and biomedical information. What does NCBI do? 

•Develop and maintain molecular and bibliographic databases.
•Develop software for searching and analysis of these data.
•Provide Web access point for data and software.

NCBI Resources and Tools

Entrez integrated literature and molecular databases
BLAST sequence similarity search service
VAST structure similarity searches
Cn3D 3D structure viewer
Genome Workbench standalone sequence analysis annotation platform
– SRA Run Browser web access for viewing searching and downloading next-generation reads
–SRA toolkit standalone SRA manipulator and client
Reference Tools

Limits and search fields, available for Nucleotide, Genome, Protein, Structure can be found here

Fields available for all Sequence Databases (Nucleotide, Protein, EST, GSS)

PubMed search fields description and tags can be found here.

Genbank sample record containing detailed description of each that data element or field

GEO Datasets and GEO Profiles query fields and examples

Structure (Molecular Modeling Database) search fields

RefSeq accession numbers can be distinguished from GenBank accessions by their distinct prefix format of 2 characters followed by an underscore character ('_')

OMIM catalog search fields are sumarized in this table. Here is the OMIM numbering system

GenBank Accession numbers for nucleotide, protein, WGS, MGA

Sequence Viewer symbol and color legend

Quick Guide to Entrez Databases

Entrez is NCBI’s primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation, and gene expression.
•Protein and Nucleic acid structures
•Small Molecules
•Medical Genetics
The NCBI Youtube Tutorials Channel contains a series of video tutorials on NCBI databases and tools including BLAST, Sequence Viewer, etc.
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