Resource
|
Description
|
| Database
retrieval tools |
|
| Entrez |
Integrated database and retrieval
system (2) for access to publicly available GenBank and other sequence data,
mapping and complete genome data, 3-D structures, and the biomedical
literature through PubMed and OMIM. |
| The Taxonomy Browser |
Search tool for the NCBI taxonomy
database which indexes over 79 000 organisms represented in the sequence
databases with at least one nucleotide or protein sequence. |
| LocusLink |
Database of official gene names
and other gene identifiers offering a single query interface to
curated sequences and descriptive information about genes, developed
with international collaborators (7). |
| The BLAST
family of sequence similarity search programs |
|
| BLAST |
The BLAST family of programs (including
BLAST, PSI-BLAST, PHI-BLAST, BLAST2Sequences) perform rapid sequence-similarity
searches of GenBank and specialized data sets (8–10). |
| Resources
for gene-level sequences |
|
| UniGene |
The UniGene system (12) partitions
GenBank sequences, including ESTs, into a non-redundant set of gene-oriented
clusters; currently includes human, mouse, rat and zebrafish. |
| HomoloGene |
A database of sets of homologous
and orthologous UniGene clusters for human, mouse, rat, zebrafish and
cow. |
| RefSeq |
Database of reference sequence
standards for mRNAs and proteins in the Entrez databases, curated
by NCBI staff (7). |
| dbSNP |
Database of Single Nucleotide
Polymorphisms (dbSNP) that includes both single base nucleotide substiutions
and short deletion and insertion polymorphisms deposited by the
scientific community (15). |
| ORF Finder |
Tool that performs a six-frame
translation of a nucleotide query and returns a graphic that indicates
the location of each ORF found. |
| Electronic PCR |
Tool for locating STSs within
a nucleotide sequence query by comparing the query with the dbSTS database
of sequences and primer pairs. |
| Resources
for chromosomal sequences |
|
| Human Genome MapViewer |
Genome browser showing an integrated
view of the human genome maps, including both physical and genetic
maps. |
| Human Genome Sequencing |
Tracks progress and provides access
to human genome sequencing data such as individual contigs and assemblies
deposited by the Human Genome Project sequencing centers. |
| GeneMap’99 |
GeneMap’99 presents mapping
information for 30 261 unique gene loci representing approximately
half of the 60 000–80 000 genes contained in the human
genome (13). |
| The Human-Mouse Homology
Maps |
Access to tables of genetic loci
in homologous segments of DNA from human and the mouse. |
| The Cancer Chromosome
Aberration Project (cCAP) |
Compilation by F. Mitelman, F.
Mertens and B. Johansson of recurrent neoplasia-associated chromosomal
aberrations from the Cancer Chromosome Aberration Bank at the University
of Lund, Sweden (18). |
| Resources
for genome-scale analysis |
|
| Entrez Genomes |
The Entrez Genomes database (20)
organizes and provides access to contributed to genomic mapping and
sequence data for over 900 species. |
| Clusters of Orthologous
Groups (COGs) |
Clusters of orthologous groups
of proteins from completely sequenced bacteria, archaea, and eukaryote (20). |
| Retroviral Genotyping
Tools |
A web-based genotyping system
for the analysis of retroviral genomes. |
| Resources
for the analysis of patterns of gene expression and phenotypes |
|
| The Cancer Genome
Anatomy Project (CGAP) |
Provides access to genetic data
on normal, precancerous and malignant cells. |
| Gene Expression Omnibus
(GEO) |
A database for gene expression
data obtained using a variety of experimental technologies such
as gene-chips and SAGE (Serial Analysis of Gene Expression). |
| SAGEmap |
SAGEmap offers many functions
for the analysis of data generated by the SAGE technique. |
| Online Mendelian
Inheritance in Man (OMIM) |
Catalog of human genes and disorders,
authored and edited by Dr Victor A. McKusick and colleagues at Johns
Hopkins University (22). |
| Molecular
structure |
|
| The Conserved Domain
Database (CDD) |
The CDD combines data from the
SMART and Pfam protein domain databases in the form of a library
of PSI-BLAST PSSMs representative of each conserved domain. This
library can be searched using NCBI’s RPS-BLAST. |
| The Molecular Modeling Database (MMDB) |
MMDB (3) is a structural database derived from
the Protein Data Bank and accessible via the Entrez system. |
