The Basic Local Alignment Search Tool (BLAST), for comparing gene and protein sequences against others in public databases, now comes in several flavors including PSI-BLAST, PHI-BLAST, and BLAST 2 sequences. Specialized BLASTs are also available for human, microbial, malaria, and other genomes, as well as for vector contamination, immunoglobulins, and tentative human consensus sequences.

Clusters of Orthologous Groups (COGs) currently covers 21 complete genomes from 17 major phylogenetic lineages. A COG is a cluster of very similar proteins found in at least three species. The presence or absence of a protein in different genomes can tell us about the evolution of the organisms, as well as point to new drug targets.

Map Viewer shows integrated views of chromosome maps for 17 organisms. Used to view the NCBI assembly of complete genomes, including human, Map Viewer is a valuable tool for the identification and localization of genes, particularly those that contribute to diseases.

LocusLink combines descriptive and sequence information on genetic loci through a single query interface. LocusLink covers information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, OMIM numbers, UniGene clusters, homology, map information, and related Web sites.

A UniGene cluster is a non-redundant set of sequences that represents a unique gene. Well-characterized genes, as well as thousands of expressed sequence tag (EST) sequences have been included. Each cluster record also contains information such as the tissue types in which the gene has been expressed and map location. UniGene can assist in gene discovery, gene mapping projects, and large-scale expression analysis.

ORF finder identifies all possible ORFs in a DNA sequence by locating the standard and alternative stop and start codons. The deduced amino acid sequences can then be used to BLAST against GenBank. ORF finder is also packaged in the sequence submission software Sequin.

Electronic PCR allows you to search your DNA sequence for sequence tagged sites (STSs), which have been used as landmarks in various types of genomic maps. It compares the query sequence against data in NCBI's UniSTS, a unified, non-redundant view of STSs from a wide range of sources.

VAST Search is a structure–structure similarity search service. It compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database. VAST Search computes a list of similar structures that can be browsed interactively, using molecular graphics to view superimpositions and alignments.

The Cancer Chromosome Aberration Project (CCAP) compiles information on the distinct chromosome aberrations that are associated with different cancers. The identification of chromosomal abnormalities by clinicians can enable the diagnosis of, classification of, and treatment selection for a given cancer.

The Human–Mouse Homology Maps compare genes in homologous segments of DNA from human and mouse sources, sorted by position in each genome. A total of 1,793 loci are presented, most of which are genes. This map should be interpreted as a reflection of probable, not confirmed, homology relationships because of the lack of further information available for about half the loci.

VecScreen is a tool for identifying segments of a nucleic acid sequence that may be of vector, linker, or adapter origin prior to sequence analysis or submission. VecScreen was developed to combat the problem of vector contamination in public sequence databases.

dbMHC provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibilty Complex (MHC). In addition, the dbMHC will provide tools for further submission and analysis of research data linked to the MHC.

Spidey aligns one or more mRNA sequences to a single genomic sequence. Spidey will try to determine the exon/intron structure, returning one or more models of the genomic structure, including the genomic/mRNA alignments for each exon.

The Cancer Genome Anatomy Project (CGAP) aims to decipher the molecular anatomy of cancer cells. CGAP develops profiles of cancer cells by comparing gene expression in normal, precancerous, and malignant cells from a wide variety of tissues.

Revised: December 4, 2003.