Data & Software


NCBI C++ Toolkit Manual

A comprehensive manual on the NCBI C++ toolkit, including its design and development framework, a C++ library reference, software examples and demos, FAQs and release notes. The manual is searchable online and can be downloaded as a series of PDF documents.

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. Searching this database is equivalent to a site search tool for the whole NCBI web site, with the exception of the FTP directories.


BLAST executables for local use are provided for Solaris, LINUX, Windows, and MacOSX 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 under the db subdirectory.

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.


This site provides full data records for CDD, along with individual Position Specific Scoring Matrices (PSSMs), mFASTA sequences and annotation data for each conserved domain. See the README file for full details.

FTP: ClinVar Data

This site provides full data extractions in XML and summary data in VCF format. It contains files with information about standard terms used in ClinVarMedGen, and GTR.


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.

FTP: GenBank

This site contains files for all sequence records in GenBank in the default flat file format. The files are organized by GenBank division, and the full contents are described in the README.genbank file.

FTP: GenPept

The protein sequences corresponding to the translations of coding sequences (CDS) in GenBank are collected for each GenBank release..Please see the README file in the directory for more information.

FTP: Gene

This site contains three directories: DATA, GeneRIF and tools. The DATA directory contains files listing all data linked to GeneIDs along with subdirectories containing ASN.1 data for the Gene records. The GeneRIF (Gene References into Function) directory contains PubMed identifiers for articles describing the function of a single gene or interactions between products of two genes. Sample programs for manipulating gene data are provided in the tools directory. Please see the README file for details.

FTP: Gene Expression Omnibus (GEO) Profiles and Datasets

This site contains GEO data in two formats: SOFT (Simple Omnibus in Text Format) and MINiML (MIAME Notation in Markup Language). Summary text files and supplementary data are also available. Please see the README.TXT file for more information.

FTP: Genome

This site contains genome sequence and mapping data for organisms in Entrez Genome. The data are organized in directories for single species or groups of species. Mapping data are collected in the directory MapView and are organized by species. See the README file in the root directory and the README files in the species subdirectories for detailed information.

FTP: Genome Mapping Data

Contains directories for each genome that include available mapping data for current and previous builds of that genome.

FTP: HomoloGene

This site contains data for each build of HomoloGene, beginning with build 35. Complete data for each build are provided in XML, and a data summary is provided in tab-delimited text format.

FTP: NCBI Taxonomy

This site contains the full taxonomy database along with files associating nucleotide and protein sequence records with their taxonomy IDs. See the taxdump_readme.txt and gi_taxid.readme files for more information.

FTP: Protein Clusters

This site contains data from the Protein Clusters database arranged by release date. See the README files for more information.

FTP: PubChem

This site provides data from the PubChem Substance, Compound and Bioassay databases for download via ftp. Full downloads of the databases are available along with daily, weekly and monthly updates for Substance and Compound. Substance and Compound data are provided in ASN.1, SDF and XML formats. See the README files for more information.

FTP: RefSeq

This site contains all nucleotide and protein sequence records in the Reference Sequence (RefSeq) collection. The ""release"" directory contains the most current release of the complete collection, while data for selected organisms (such as human, mouse and rat) are available in separate directories. Data are available in FASTA and flat file formats. See the README file for details.

FTP: SKY/M-Fish and CGH Data

This site contains SKY-CGH data in ASN.1, XML and EasySKYCGH formats. See the skycghreadme.txt file for more information.


Downloadable data for SNP.

FTP: Sequence Read Archive (SRA) Download Facility

This site contains next-generation sequencing data organized by the submitted sequencing project.

FTP: Site

FTP download site for NCBI databases, tools, and utilities.

FTP: Structure (MMDB)

This site contains ASN.1 data for all records in MMDB along with VAST alignment data and the non-redundant PDB (nr-PDB) data sets. See the README file for more information.

FTP: Trace Archive

This site contains the trace chromatogram data organized by species. Data include chromatogram, quality scores, FASTA sequences from automatic base calls, and other ancillary information in tab-delimited text as well as XML formats. See the README file for details.

FTP: UniGene

This site contains individual directories for each organism with data in UniGene. The data for each species includes the unique sequence for each UniGene cluster, all sequences in each cluster in FASTA format and library information for the cluster. See the README file for further details.

FTP: UniVec

This site contains the UniVec and UniVec_Core databases in FASTA format. See the README.uv file for details.

FTP: Whole Genome Shotgun Sequences

This site contains whole genome shotgun sequence data organized by the 4-digit project code. Data include GenBank and GenPept flat files, quality scores and summary statistics. See the README.genbank.wgs file for more information.

FTP: dbGAP Open-Access Data

Open-access data generally include summaries of genotype/phenotype association studies, descriptions of the measured variables, and study documents, such as the protocol and questionnaires. Access to individual-level data, including phenotypic data tables and genotypes, requires varying levels of authorization.

FTP: dbMHC Data

This site contains data in separate directories for the various projects and resources within the database of human major histocompatibility (dbMHC).

NCBI Data Specifications

Specifications for NCBI data in ASN.1 or DTD format are available on the Index of data_specs page. The "NCBI_data_conversion.html" links to the conversion tool.

National Library of Medicine (NLM) DTDs

A suite of tag sets for authoring and archiving journal articles as well as transferring journal articles from publishers to archives and between archives. There are four tag sets: Archiving and Interchange Tag Set - Created to enable an archive to capture as many of the structural and semantic components of existing printed and tagged journal material as conveniently as possible; Journal Publishing Tag Set - Optimized for archives that wish to regularize and control their content, not to accept the sequence and arrangement presented to them by any particular publisher; Article Authoring Tag Set - Designed for authoring new journal articles; NCBI Book Tag Set - Written specifically to describe volumes for the NCBI online libraries.

PubChem Download Service

This service allows users to download compound or substance records corresponding to a set of PubChem identifiers, which can be supplied manually or through a text file. Numerous download formats are available, including SDF, XML and SMILES.

RSS Feeds

Subscribe to Web/RSS feeds for updates about NCBI resources.


BioProject Submission

An online form that provides an interface for researchers, consortia and organizations to register their BioProjects. This serves as the starting point for the submission of genomic and genetic data for the study. The data does not need to be submitted at the time of BioProject registration.

A web-based sequence submission tool for one or a few submissions to the GenBank database, designed to make the submission process quick and easy.

GenBank: Barcode

Tool for submission to the GenBank database of Barcode short nucleotide sequences from a standard genetic locus for use in species identification.

A stand-alone software tool developed by the NCBI for submitting and updating entries to public sequence databases (GenBank, EMBL, or DDBJ). It is capable of handling simple submissions that contain a single short mRNA sequence, complex submissions containing long sequences, multiple annotations, segmented sets of DNA, as well as sequences from phylogenetic and population studies with alignments. For simple submission, use the online submission tool BankIt instead.

A command-line program that automates the creation of sequence records for submission to GenBank using many of the same functions as Sequin. It is used primarily for submission of complete genomes and large batches of sequences.

Gene Expression Omnibus (GEO) Web Deposit

Submit expression data, such as microarray, SAGE or mass spectrometry datasets to the NCBI Gene Expression Omnibus (GEO) database.

PubChem Upload

This site enables users to submit data to the PubChem Substance and BioAssay databases, including chemical structures, experimental biological activity results, annotations, siRNA data and more. It can also be used to update previously submitted records.

The SNP database tools page provides links to the general submission guidelines and to the submission handle request. The page has also two specific links for single- or batch submissions of the human variation data using Human Genome Variation Society nomenclature.

Submission Portal

A single entry point for submitters to link to and find information about all of the data submission processes at NCBI. Currently, this serves as an interface for the registration of BioProjects and BioSamples and submission of data for WGS and GTR. Future additions to this site are planned.

Trace Archive Submission

This link describes how submitters of trace data can obtain a secure NCBI FTP site for their data, and also describes the allowed data formats and directory structures.


BLAST Microbial Genomes

Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes.

BLAST RefSeqGene

Performs a BLAST search of the genomic sequences in the RefSeqGene/LRG set. The default display provides ready navigation to review alignments in the Graphics display.

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.

Batch Entrez

Allows you to retrieve records from many Entrez databases by uploading a file of GI or accession numbers from the Nucleotide or Protein databases, or a file of unique identifiers from other Entrez databases. Search results can be saved in various formats directly to a local file on your computer.


A stand-alone application for classifying protein sequences and investigating their evolutionary relationships. CDTree can import, analyze and update existing Conserved Domain (CDD) records and hierarchies, and also allows users to create their own. CDTree is tightly integrated with Entrez CDD and Cn3D, and allows users to create and update protein domain alignments.


COBALT is a protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST.

A stand-alone application for viewing 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, Macintosh, and UNIX and can be configured to receive data from most popular web browsers. Cn3D simultaneously displays structure, sequence, and alignment, and has powerful annotation and alignment editing features.

Concise Microbial Protein BLAST

A specialized BLAST service in which the queried database consists of all proteins from complete microbial (prokaryotic) genomes. NCBI has precalculated clusters of similar proteins at the genus-level and one representative is chosen from each cluster in order to reduce the dataset, thereby reducing search time and providing a broader taxonomic view.

Identifies the conserved domains present in a protein sequence. CD-Search uses RPS-BLAST (Reverse Position-Specific BLAST) to compare a query sequence against position-specific score matrices that have been prepared from conserved domain alignments present in the Conserved Domain Database (CDD).

Tools that provide access to data within NCBI's Entrez system outside of the regular web query interface. They provide a method of automating Entrez tasks within software applications. Each utility performs a specialized retrieval task, and can be used simply by writing a specially formatted URL.

Frequency-weighted Link (FLink)

FLink is a tool that enables you to link from a group of records in a source database to a ranked list of associated records in a destination database based on frequency-weighted statistics.

Gene Expression Omnibus (GEO) BLAST

Tool for aligning a query sequence (nucleotide or protein) to GenBank sequences included on microarray or SAGE platforms in the GEO database.

Genome BLAST

This tool compares nucleotide or protein sequences to genomic sequence databases and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST) algorithm.

Genome ProtMap maps each protein from a COG, or in the case of viruses a VOG, back to its genome, and displays all the genomic segments coding for members of this particular group of related proteins. The view can be shifted to focus on an adjacent COG/VOG, and clusters can be searched by name, protein gi, or gene locus tag.

Genome Remapping Service

NCBI's Remap tool allows users to project annotation data and convert locations of features from one genomic assembly to another or to RefSeqGene sequences through a base by base analysis. Options are provided to adjust the stringency of remapping, and summary results are displayed on the web page. Full results can be downloaded for viewing in NCBI's Genome Workbench graphical viewer, and annotation data for the remapped features, as well as summary data, is also available for download.

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.

NCBI Toolbox

A set of software and data exchange specifications used by NCBI to produce portable, modular software for molecular biology. The software in the Toolbox is primarily designed to read records in Abstract Syntax Notation 1 (ASN.1) format, an International Standards Organization (ISO) data representation format.


A public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols. OSIRIS evaluates the raw electrophoresis data using an independently derived mathematically-based sizing algorithm. It offers two new peak quality measures - fit level and sizing residual. It can be customized to accommodate laboratory-specific signatures such as background noise settings, customized naming conventions and additional internal laboratory controls.

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.

The Primer-BLAST tool uses Primer3 to design PCR primers to a sequence template. The potential products are then automatically analyzed with a BLAST search against user specified databases, to check the specificity to the target intended.

A utility for computing alignment of proteins to genomic nucleotide sequence. 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, ProSplign is accurate in determining splice sites and tolerant to sequencing errors.

PubChem Power User Gateway (PUG)

PUG provides access to PubChem services via a programmatic interface. PUG allows users to download data, initiate chemical structure searches, standardize chemical structures and interact with the E-utilities. PUG can be accessed using either standard URLs or via SOAP.

PubChem Standardization Service

Standardization, in PubChem terminology, is the processing of chemical structures in the same way used to create PubChem Compound records from contributors' original structures. This service lets users see how PubChem would handle any structure they would like to submit.

PubChem Structure Search allows the PubChem Compound Database to be queried by chemical structure or chemical structure pattern. The PubChem Sketcher allows a query to be drawn manually. Users may also specify the structural query input by PubChem Compound Identifier (CID), SMILES, SMARTS, InChI, Molecular Formula, or by upload of a supported structure file format.

SNP Database Specialized Search Tools

A variety of tools are available for searching the SNP database, allowing search by genotype, method, population, submitter, markers and sequence similarity using BLAST. These are linked under ""Search"" on the left side bar of the dbSNP main page.

Sequence Viewer

Provides a configurable graphical display of a nucleotide or protein sequence and features that have been annotated on that sequence. In addition to use on NCBI sequence database pages, this viewer is available as an embeddable webpage component. Detailed documentation including an API Reference guide is available for developers wishing to embed the viewer in their own pages.

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.

Variation Reporter

A tool designed to search human sequence variation data by location and to report matching variants found in dbSNP, dbVar and ClinVar. Individual variations or batch files can be submitted in HGVS, GVF, VCS or BED formats. Related information will be reported in a downloadable table containing variation identifiers, nucleotide and cytogenetic band locations on various genomic assemblies, allele type and minor allele frequencies, predicted functional consequences (missense, nonsense, frameshift, splice site, etc.), reported clinical significance, and relevant citations. For variants not present in the NCBI variation resources, the tool computes molecular consequences based on RefSeq transcripts.


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).

A computer algorithm that identifies similar protein 3-dimensional structures. Structure neighbors for every structure in MMDB are pre-computed and accessible via links on the MMDB Structure Summary pages. These neighbors can be used to identify distant homologs that cannot be recognized by sequence comparison alone.