NCBI (National center for biotechnology information)

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Created as a part of NLM in 1988
Establish public databases
Research in computational biology
Develop software tools for sequence analysis
Disseminate biomedical information
Tools: BLAST(1990), Entrez (1992)
GenBank (1992)
Free MEDLINE (Pub Med, 1997)
Human genome (2001)

Hot Spots

Assembly Archive

Clusters of orthologous groups

Coffee Break, Genes & Disease,
NCBI Handbook

Electronic PCR

Entrez Home

Entrez Tools

Gene expression omnibus (GEO)

Human genome resources

Influenza Virus Resource

Map Viewer

dbMHC

My NCBI

ORF finder

Rat genome resources

Reference sequence project

Basic Research

To develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that control health and disease

Creating automated systems for storing and analyzing knowledge about molecular biology, biochemistry, and genetics

Facilitating the use of such databases and software by the research and medical community; coordinating efforts to gather biotechnology information both nationally and internationally

Performing research into advanced methods of computer-based information processing for analyzing the structure and function of biologically important molecules


Organisation structure

NCBI branches
Computational Biology Branch (CBB)
Conducts basic and applied research in

Computational, mathematical, and theoretical problems in molecular biology and genetics
Genome analysis
Sequence comparisons
Sequence search methodologies
Macromolecular structure
Dynamics and interaction, and structure/function prediction

Information Engineering Branch (IEB)

Performs applied research in data representation and analysis

Includes the development of computer-based systems for the storage, management, and retrieval of knowledge relating to molecular biology, genetics, and biochemistry
Designs database schema and specifications for representation of various forms of molecular biology information, including nucleic acid, protein, and structural information. These databases serve as national resources.

Information Resources Branch (IRB)

Plans, directs, and manages the technical operations of NCBI
Computer systems used for research and development as well as the computer systems used to access public databases
Provides technical assistance to NCBI staff and provides support for external users of NCBI network services
Supervises network operations for the NCBI and coordinates with other government agencies for both national and international access to NCBI services


Entrez:

An Integrated Database Search and Retrieval System

Nucleotide Sequences Database

Entrez Nucleotides - combines data from a number of source databases, including GenBank, RefSeq, TPA, and PDB. Data can be searched by accession number, author name, organism, gene/protein name, and a variety of other text terms

GenBank - a database of nucleotide sequences from >160,000 organisms. Records that are annotated with coding region (CDS) features also include amino acid translations.

RefSeq - NCBI database of Reference Sequences. Curated, non-redundant set including genomic DNA contigs, mRNAs and proteins for known genes, mRNAs and proteins for gene models, and entire chromosomes.
Note : Accession numbers have the format of two letters, an underscore bar, and six digits. Nucleotide sequence records have accessions: NT_123456, NM_123456, NC_123456, NG_123456, XM_123456, XR_123456


Sequences Database

dbEST - database of expressed sequence tags; short, single cDNA (mRNA) sequences. Also includes cDNA sequences from differential display experiments and RACE experiments.
dbGSS - database of genome survey sequences; short, single pass read genomic sequences, exon trapped sequences, cosmid/BAC/YAC ends, others.
dbMHC - Provides a platform where the human leukocyte antigen (HLA) community can submit, edit, view, and exchange Major Histocompatibility Complex (MHC) data.
dbSNP - database of single nucleotide polymorphisms, small-scale insertions/deletions, polymorphic repetitive elements, and microsatellite variation.
dbSTS - database of sequence tagged sites; short sequences that are operationally unique in the genome, used to generate mapping reagents

Protein Sequence Databases

Entrez Proteins - search protein sequence records (from GenPept + RefSeq + Swiss-Prot + PIR + PDB) by accession number, author name, organism, gene/protein name, and a variety of other text terms.

RefSeq - NCBI database of Reference Sequences. non-redundant set including genomic DNA contigs, mRNAs and proteins for known genes,

FTP GenPept

Conserved Domain Database (CDD) - a collection of sequence alignments and profiles representing protein domains conserved in molecular evolution.

HIV Interactions - The HIV-1, Human Protein Interaction Database contains information about known interactions of HIV-1 proteins with proteins from human hosts.

PROW - Protein Resources on the Web - short authoritative guides on the approximately 200 human CD cell-surface molecules.

Expression Database

Gene Expression Omnibus (GEO) - a gene expression and hybridization array data repository.

GENSAT - The Gene Expression Nervous System Atlas, or GENSAT, project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques

SAGE map - Serial Analysis of Gene Expression, or SAGE, is an experimental technique designed to quantitatively measure gene expression.

CGAP - Cancer Genome Anatomy Project - interdisciplinary program to identify the human genes expressed in different cancerous states, based on cDNA (EST) libraries, and to determine the molecular profiles of normal, precancerous, and malignant cells.

UniGene DDD - Digital Differential Display - an online tool to compare computed gene expression profiles between selected cDNA libraries.

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