Databases

BioSystems
Database that groups biomedical literature, small molecules, and sequence data in terms of biological relationships.
GenBank
The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. GenBank consists of several divisions, most of which can be accessed through the Nucleotide database. The exceptions are the EST and GSS divisions, which are accessed through the Nucleotide EST and Nucleotide GSS databases, respectively.
NCBI Website Search
A database of static NCBI web pages, documentation, and online tools. These pages include such content as specialized online sequence analysis tools, back issues of newsletters, legacy resource description pages, sample code, and other miscellaneous resources.
Peptidome
A public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Includes identified proteins, identified peptides for protein identification, mass spectra that support identifications, and supporting documentation.

Tools

BLAST (Basic Local Alignment Search Tool)
Finds regions of local similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families.
BLAST Link (BLink)
A link option on protein records that displays the results of a pre-computed BLAST search of that protein against all other protein sequences at NCBI.
BLAST Microbial Genomes
Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes.
Genome Workbench
An integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix these data with your own data.
Influenza Virus
Presents data from the NIAID Influenza Genome Sequencing Project and from GenBank, and provides tools for flu sequence analysis, annotation and submission to GenBank. It also provides links to other flu sequence resources, and publications and general information about flu viruses.
Open Reading Frame Finder (ORF Finder)
A graphical analysis tool that finds all open reading frames in a user's sequence or in a sequence already in the database. Sixteen different genetic codes can be used. The deduced amino acid sequence can be saved in various formats and searched against protein databases using BLAST.
Splign
A utility for computing cDNA-to-Genomic sequence alignments. It is based on a variation of the Needleman-Wunsch global alignment algorithm and specifically accounts for introns and splice signals. Due to this algorithm, Splign is accurate in determining splice sites and tolerant to sequencing errors.
Trace Mega BLAST
Compares nucleotide sequence data against the raw data underlying all of the sequences generated by various genome projects.
VecScreen
A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. VecScreen searches a query sequence for segments that match any sequence in a specialized non-redundant vector database (UniVec).

Downloads

BLAST (Stand-alone)
BLAST executables for local use are provided for IRIX 6.2, Solaris 2.6, DEC OSF1 (ver. 4.0d), LINUX, and Win32 systems. See the README file in the ftp directory for more information. Pre-formatted databases for BLAST nucleotide, protein, and translated searches also are available for downloading.
FTP: BLAST Databases
Sequence databases for use with the stand-alone BLAST programs. The files in this directory are pre-formatted databases that are ready to use with BLAST.
FTP: FASTA BLAST Databases
Sequence databases in FASTA format for use with the stand-alone BLAST programs. These databases must be formatted using formatdb before they can be used with BLAST.