• What's New - recently released resources and enhancements to existing resources.

• NCBI News - announcements about new resources, enhancements to existing resources, staff publications, tutorials, FAQs.

• NCBI Announcements Email Lists - Receive announcements about changes and updates to a variety of NCBI services. In addition to a general NCBI-announce list, topic-specific e-mail lists are available for BLAST, GenBank, dbSNP, Genomes, LinkOut, RefSeq, Sequin, and Entrez Utilities (for making WWW Links to Entrez). Follow the link to the NCBI Announcements Email Lists page to see a complete list of available topics. Information on how to subscribe is provided.

• NCBI RSS Feeds - Receive announcements about various NCBI services using an RSS (Real simple syndication) feed reader. RSS feeds are available for resources such as Bookshelf, HomoloGene, PubMed Central, PubMed New and Noteworthy, Probe Database, and UniGene. Follow the link to the NCBI RSS Feeds page to see a complete list of available topics. Additional information about RSS is provided in a short series of FAQs.

General Information (sample record, release notes, GenBank divisions, statistics),   Submissions (general, special categories, other data types),   International Collaboration,   FTP GenBank

• General information about submitting nucleotide sequence data to GenBank, receiving accession numbers, and making updates to records. Special types of submissions to GenBank, such as genomes, alignments, ESTs, GSSs, HTGs, STSs, and WGS are discussed below.

In addition to GenBank, there are other databases at NCBI to which a variety of data types can be submitted (third party annotations (TPA), variation, expression, MHC data, SKY/M-FISH/CGH data, traces).

• BankIt - WWW submission tool for one or few submissions, designed to make the submission process quick and easy.  (BankIt also automatically uses VecScreen to identify segments of nucleic acid sequence which may be of vector, adapter, or linker origin to combat the problem of vector contamination in GenBank.)

• Sequin - submission software program for one or many submissions, long sequences, complete genomes, alignments, population/phylogenetic/mutation studies. Can be used as a stand-alone application or in a TCP/IP-based "network aware" mode, with links to other NCBI resources and software such as Entrez.  (Use VecScreen prior to submission).  To receive announcements about updates to the Sequin submission software, see the NCBI Announcements Email Lists page.

• Submission of complete genomes and other large sequence records - Recent enhancements to Sequin make it convenient for genome sequencing centers to annotate their records with Sequin and submit the resulting ASN.1 file to GenBank. After the Sequin files are prepared, large genomes should be submitted by ftp; write to genomes@ncbi.nlm.nih.gov to obtain an ftp account. Smaller records less than 350 kb can be sent by email to gb-sub@ncbi.nlm.nih.gov.
  
  More information about submitting genomes and other large sequence records is provided on the following pages: GenBank submissions, Sequin, tabular layout for submitting annotated features, bacterial genome submission guidelines.
  
  In addition, sequencing centers can register a sequencing project with NCBI prior to the submission of any data. This can be done through a Genome project submission form. For each registered project, NCBI will create a sequencing project page that describes the project, links out to genome-specific reosurces, and provides a focal point for the addition of links to NCBI resources such as Map Viewer and genomic BLAST. Projects can be listed publicly or remain unlisted, and sequences may be held until publication (the default), released immediately, or made available for BLAST searches only. The form can also be used to set up an FTP site for the upload of data to NCBI, or to specify a URL to be used by NCBI for download of project or sequence data. (See Fall 2003/Winter 2004 issue of NCBI News for more information.)

• Alignments - submission of aligned sequences from population, phylogenetic, or mutation studies. Several sections of the Sequin Help Documentation also include information on how to submit alignments, such as Submission Type, FAST A+GA P Format for Aligned Nucleotide Sequences, PHYLIP Format for Aligned Nucleotide Sequences, NEXUS Format for Aligned Nucleotide Sequences, Source Modifiers for PHYLIP and NEXUS, Importin g Aligned Sets of Segmented Sequences. Check the Sequin help documentation for other relevant sections. (See Fall 2003/Winter 2004 issue of NCBI News for an example in the "Submissions Corner".)

• ESTs - expressed sequence tags; short, single pass read cDNA (mRNA) sequences. Also includes cDNA sequences from differential display experiments and RACE experiments.

• GSSs - genome survey sequences; short, single pass read genomic sequences, exon trapped sequences, cosmid/BAC/YAC ends, others.

• HTGs - high throughput genome sequences from large scale genome sequencing centers; unfinished (phase 0, 1, 2) and finished (phase 3) sequences. (Note that contigs assembled from draft and finished human HTG sequences are accessible from the Map Viewer, described below.)

• STSs - sequence tagged sites; short sequences that are operationally unique in the genome, used to generate mapping reagents.

• WGS - data from Whole Genome Shotgun (WGS) sequencing projects can be submitted to GenBank. The data can contain annotations and an entire project is updated as sequencing progresses. WGS submissions are given accession numbers in the format of four letters followed by eight digits, e.g., XXXX00000000. The four letters are a stable project_ID, which does not change as the project is updated. The first two digits represent the version number, which corresponds to a particular project update. The last six digits represent an individual contig within the WGS project. For example, if a project's assigned accession number is XXXX00000000, then that project's first assembly version would be XXXX01000000, and the first contig of that version would be XXXX01000001. (more...)
  The nucleotide data from WGS projects go into the appropriate organismal GenBank Divisions and the BLAST wgs database. The protein translations of annotated coding sequences go into the BLAST protein nr database. In addition, quality data from many WGS projects are submitted to the Trace Archive (described in the ResourceGuide section on Nucleotide Sequence Databases).

• Third Party Annotations (TPA) - a database of experimentally supported annotations on assemblies of sequences already present in DDBJ/EMBL/GenBank. Whereas DDBJ/EMBL/GenBank contains primary sequence data and corresponding annotations submitted by the laboratories that did the sequencing, the TPA database contains third-party assemblies of primary data with experimentally supported annotation that has been published in a peer-reviewed scientific journal. Details about how to submit data, as well as examples of what can and cannot be submitted to TPA, are provided on the TPA home page. Additional information about the TPA database is provided below.

• Genetic Variation - in humans and other organisms can be submitted to the NCBI Database of Single Nucleotide Polymorphisms (dbSNP).  Although dbSNP is a separate database from GenBank, as noted above, SNP records include cross-references to GenBank records.  (submission instructions)  Additional information about dbSNP is below.

• Gene Expression - data can be submitted to Gene Expression Omnibus (GEO)  (submission instructions).  Additional information about GEO is below.

• Major Histocompatibility Complex (MHC) - DNA sequence and clinical data can be submitted to dbMHC.   A brief description of dbMHC is provided in the Molecular Databases/Nucleotide Sequences section of this guide, and additional details are available in the NCBI Handbook.

• Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic Hybridization (CGH) - data can be submitted to the NCI and NCBI SKY/M-FISH & CGH Database  (submission instructions)  Additional information about the NCI and NCBI SKY/M-FISH & CGH Database is below.

• Trace Data - can be submitted to the Trace Archive, a repository of the raw sequence traces generated by large sequencing projects.  (submission instructions)  Additional information about the Trace Archive is below.

Nucleotide Sequences,   Protein Sequences,   Structures,   Genes,   Expression,   Taxonomy

Consensus CoDing Sequence (CCDS) Database - The CCDS project is a collaborative effort to identify a core set of human protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations on the human genome. The collaborators include the National Center for Biotechnology Information (NCBI, Map Viewer), European Bioinformatics Institute (EBI, Ensembl), University of California, Santa Cruz (UCSC, Genome Browser), and Wellcome Trust Sanger Institute (WTSI, Vega). They identify the position of protein-coding regions of genes that are (1) annotated consistently on the human genome by all of the participating centers and (2) supported by transcript evidence, use of canonical splice sites, and other quality assurance measures. Additional information about the curation, process flow, and quality testing is available on the CCDS web site.

Note:  Although TPA records are derived from DDBJ/EMBL/GenBank, TPA is actually a separate database. Therefore, TPA records are not present in the GenBank FTP files, but will be available in separate FTP files.

The TPA database uses an accession format similar to GenBank records (e.g., two letters followed by six digits) and is organized into similar divisions. (A list of GenBank divisions is given in the GenBank Sample Record. Some divisions, such as EST, GSS, HTG and are present in GenBank but will not be present in TPA.)

TPA records can be easily recognized because the definition lines begin with the the letters "TPA", and they contain "Third Party Annotation; TPA" in the Keywords field. This is illustrated in a sample TPA record, BK000627.

TPA records can be retrieved from Entrez Nucleotides (described above). To only see data from TPA, use the "Index" mode to select "tpa" from the Properties search field, or simply add the command AND tpa[prop] to your query.

Details about how to submit data, as well as examples of what can and cannot be submitted to TPA, are provided on the TPA home page. An announcement and additional information about the TPA database is provided in section 1.4.5, "Third-Party Annotation and Consensus Sequences (TPA)" of the GenBank 133.0 release notes.

Assembly Archive - links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ). The Assembly Viewer allows a user to see the multiple sequence alignments as well as the actual sequence chromatogram.

• Resources in the Genomes and Maps section contain annotations for the proteins encoded by a variety of genomes. Examples of the genomes available include:   >1000 organisms in Entrez Genome, human, mouse, rat, zebrafish, Drosophila, nematode, plant genomes, yeast, malaria, microbial genomes, viruses, viroids, plasmids, eukaryotic organelles. The proteomes of human, mouse, rat, and a growing number of other eukaryotes are also shown as annotations on the genomes of those organisms in Map Viewer (described in the Genomes and Maps section). MapViewer can display the data graphically or in tabular format, and also provides links to corresponding data on the FTP site.

• Entrez Genome - provides ProtTable and TaxTable for various organisms. The ProtTable provides a summary of protein coding regions in a genome, and provides links to the corresponding nucleotide and protein sequences in FASTA format. The TaxTable, also referred to as the "distribution of BLAST protein homologs by taxa," summarizes the results of BLAST analyses done for the proteins, and displays the relationship of the organism to others through a color-coded graphical summary. (Additional information about Entrez Genome is provided below.)

• FTP Genome Proteins - download an *.faa file (FASTA formatted amino acid sequences) and *ptt file (protein table) for various organisms from the genbank/genomes directory of the ftp site; see readme file for more information. Protein tables can also be viewed in Entrez Genome, as noted above.

• PubChem Substance - Primary data NCBI obtains from the various public depositories. The PubChem Substance database contains approximately 13 million records as of October 2006, provided by various sources, DTP/NCI, NIAID, ChemIDplus, NIST, NIST webbook, MOLI/NCI, ChemBank, MMDB, KEGG, and more. Substance information includes chemical structures, synonyms, registration IDs, descriptions, related urls, and database cross-reference links to PubMed, protein 3D structures, and biological screening results.

• PubChem Compound - A database made by NCBI and derived from PCSubstance. It is a non-redundant view of the chemically validated substances in PubChem Substance. There is one PubChem Compound record for each unique substance, and for each unique substance component. There can be multiple PubChem Substance records associated with one PubChem Compound record. PubChem Compound contains all standardized structures, mixture components, and precalculated structure neighboring links. Compound information includes structure, compound property information (molecular weight, formula, xLogP, count of the rotatable bonds, H bond donor, H bond acceptor, etc.), and structure description (SMILES, IUPAC name, INCHI).

• PubChem BioAssay - The assay database consists of deposited bioactivity data and descriptions of bioactivity assays used for screening of the chemical substances contained in PubChem Substance, including descriptions of the conditions and the readouts (bioactivity levels) specific to the screening procedure. The assay database includes DTP/NCI's 710 million lines of in vitro and in vivo data covering from cancer, HIV, to many other fields.

• Cn3D - "See in 3-D," a structure and sequence alignment viewer for NCBI databases. It allows viewing of 3-D structures and sequence-structure or structure-structure alignments. Cn3D can work as a helper application to your browser, or as a client-server application that retrieves structure records from MMDB (described above) directly over the internet. The Cn3D home page provides access to information on how to install the program, a tutorial to get started, and a comprehensive help document.

• CD-Search - The Conserved Domain Search Service (CD-Search) can be used to identify the conserved domains present in a protein sequence. CD-Search uses RPS-BLAST (described above) 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) (described above). Hits can be displayed as a pairwise alignment of the query sequence with a representative domain sequence, or as a multiple alignment. Alignments are also mapped to known 3-dimensional structures, and can be displayed using Cn3D (described above). In the Cn3D display, residues in sequence alignments are variously colored, based on their degree of conservation.

• VAST - Vector Alignment Search Tool - a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures. The "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.

• VAST Search - structure-structure similarity search service. Compares 3D coordinates of a newly determined protein structure to those in the MMDB/PDB database. VAST Search computes a list of structure neighbors that you may browse interactively, viewing superpositions and alignments by molecular graphics.

GeneRIF - Gene References into Function (GeneRIFs) provide a simple mechanism to allow scientists to add to the functional annotation of loci described in Entrez Gene. They appear as annotated bibliographies in Entrez Gene records, and consist of brief statements on gene function with links to the corresponding PubMed records (example: human MLH1). The GeneRIF help page describes the simple steps needed to submit information. GeneRIFs are also added to the Entrez Gene records by the MEDLINE Indexing Staff of the National Library of Medicine. GeneRIFs are currently available for a subset of organisms in Entrez Gene, and will be provided for the loci of other organisms as the development of Entrez Gene continues.

LocusLink - LocusLink was discontinued as of March 1, 2005. It provided a foundation for what is now Entrez Gene and was described in several articles ( Pruitt KD, Maglott DR (2001), Pruitt KD, Katz KS, Sicotte H, Maglott DR (2000)). It contained data for a number of species such as human, mouse, rat, zebrafish, nematode, fruit fly, cow, sea urchin, African clawed frog, HIV-1, and a few other model and commonly studied organisms. Data for these organisms (and from the ongoing collaboration among the groups listed above) are now available in the Entrez Gene database (described above), which is the successor to LocusLink. The major differences between LocusLink and Entrez Gene are scope of data and search interface. Entrez Gene contains data from all organisms with RefSeq genome records. (RefSeq is described in the Molecular Databases/Nucleotide Sequences section of this guide). Entrez Gene also uses the Entrez search system, and therefore offers the helpful functions such as Preview/Index, History, and LinkOut that are available for other Entrez databases. The Entrez Gene help document includes numerous tips for previous users of LocusLink.

• SAGEmap - Serial Analysis of Gene Expression, or SAGE, is an experimental technique designed to quantitatively measure gene expression. SAGEmap is an online tool to compare computed gene expression profiles between SAGE libraries generated by the Cancer Genome Anatomy Project (CGAP, described under human genome/cancer research) and submitted by others through the Gene Expression Omnibus (GEO, described above). SAGEmap also includes a comprehensive analysis of SAGE tags in human GenBank records, in which a UniGene identifier is assigned to each human sequence that contains a SAGE tag. Data can be retrieved by tag, by sequence, by UniGene cluster ID and by library name. When retrieving data by sequence or UniGene cluster ID, follow a SAGE tag's hotlink to find out its expression level in different SAGE libraries, and how it is represented in the rest of the sequences in GenBank. Retrieving data by library name takes one to GEO, where all SAGEmap data has been stored by library. Analytical tools include xProfiler, which compares gene expression between SAGE libraries of your choice as well as uploaded data. More information about the additional analytical capabilities of the SAGEmap resource is provided in the tools/gene expression section of this file.

• 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. Collaboration among the National Cancer Institute, the NCBI, and numerous research labs. Additional information about CGAP is provided in the tools/gene expression section of this file. Related resources are described in the human genome/cancer research section.

• UniGene DDD - Digital Differential Display - an online tool to compare computed gene expression profiles between selected cDNA libraries. Using a statistical test, genes whose expression levels differ significantly from one tissue to the next are identified and shown to the user. Additional information about UniGene is in the molecular databases/genes section.

• Journals Database - allows you to lookup journals that are cited in any of the Entrez databases, including PubMed. Journals can be searched using the journal title, MEDLINE or ISO abbreviation, ISSN, or the NLM Catalog ID.

• MeSH - The Medical Subject Headings (MeSH) database is NLM's controlled vocabulary used for indexing articles for MEDLINE/PubMed. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts.

• Citation Matcher - allows you to find the PubMed ID of any article in the PubMed database, given its bibliographic information (journal, volume, page, etc.).
• Citation Matcher for single articles
• Batch Citation Matcher for many articles

Information about submitting genome data from complete genomes is provided in the Resource Guide section on Submission of complete genomes. After data from complete genomes are submitted, they are made available in Entrez Genome (as complete genomes or chromosomes) and Entrez Nucleotide (as chromosome or genome fragments such as contigs). Entrez Nucleotide also provides access to the records for complete genomes/chromosomes, but the default view of those records is the Nucleotide database is GenBank format, whereas the default view in Entrez Genome is a graphical overview. A companion database, Entrez Genome Project, is described below.

Guide,   Chromosomes,   Sequences,   Genes,   BLAST,   Clones,   Genome Maps,   Mapped Markers,   Cytogenetics,   Gene Expression,   Genetic Variation,   Disorders,   Cancer Research,   FTP

• Human Genome Resources Guide - overview of available human genome data resources. Includes bulletins and progress reports concerning the Human Genome Project and provides centralized access to previously disparate data.

• Introduction to NCBI's Genome Resource - overview of the nature of data generated by the human genome project, the processes use to assemble and annotate the data, and to integrate it with a wide range of information from other resources.

• NCBI Contig Assembly and Annotation Process - describes the processes use to assemble contigs from the high throughput genomic sequences (HTGs, described above), and to annotate the contigs with features. It also describes the various resources that can be used to access the human genome data.

• Tour of the Draft Human Genome Sequence - provides an introduction to how the draft sequence of the human genome can be used by biologists, and includes examples of the types of questions that can be answered with the data.

• Map Viewer - integrated views of chromosome maps - The Map Viewer (described above) displays one or more maps which have been aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. For human, the Map Viewer includes >20 sequence, cytogenetic, genetic linkage, radiation hybrid, and other maps.  (When viewing a chromosome, use the "Maps & Options" dialog box to display the map(s) of interest.)   The sequence maps are based on the contigs built from the draft and finished sequence data generated by the Human Genome Project. A list of available human maps and their descriptions is provided. The Map Viewer help document provides general information on how to use that tool. Information about the NCBI Contig Assembly and Annotation Process is also available.

• FTP human chromosome data - see the FTP information, below

• Human Genome Sequencing - sequencing progress of the Human Genome Project; links to chromosome views in the Map Viewer (described above), including sequence maps assembled from contigs that were constructed (more...) from international sequencing center data; list of genome sequencing centers.

• 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. Accession numbers have the format of two letters, an underscore bar, and six digits, for example, NC_123456, NT_123456, NM_123456, NP_123456 (more info about accession numbers and access).

• Entrez - provides integrated access to nucleotide and protein sequence data in GenBank, EMBL, DDBJ, RefSeq, PIR-International, PRF, Swiss-Prot, and PDB, along with 3D protein structures, genomic mapping information, and PubMed MEDLINE. Entrez contains pre-computed similarity searches for each database record, producing a list of related sequences, structures, and MEDLINE records. Includes sequence data from >160,000 species; use the organism field to limit searches to human records.

• UniGene - ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene within the organism from which the sequences were obtained. Additional information about UniGene is provided above.

• dbEST - Database of Expressed Sequence Tags - short (about 300-500 bp) cDNA sequences representing single-pass reads from mRNA. Usually produced in large numbers and represent a snapshot of the genes expressed in a given tissue, and/or at a given developmental stage. Also includes ESTs generated by the CGAP project (see Cancer Research, below), and sequences from differential display and RACE experiments.

• Consensus CoDing Sequence (CCDS) Database - The CCDS project is a collaborative effort to identify a core set of human protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations on the human genome. The collaborators include the National Center for Biotechnology Information (NCBI, Map Viewer), European Bioinformatics Institute (EBI, Ensembl), University of California, Santa Cruz (UCSC, Genome Browser), and Wellcome Trust Sanger Institute (WTSI, Vega). They identify the position of protein-coding regions of genes that are (1) annotated consistently on the human genome by all of the participating centers and (2) supported by transcript evidence, use of canonical splice sites, and other quality assurance measures. Additional information about the curation, process flow, and quality testing is available on the CCDS web site.

• Entrez Gene - a gene-based view of the data from a wide range of genomes, including human. It supplies key connections in the nexus of map, sequence, expression, structure, functional, and homology data. More information about Entrez Gene is provided above, in the Molecular Databases/Genes section.

• OMIM - Online Mendelian Inheritance in Man - continuously updated catalog of human genes and genetic disorders, with links to associated literature references, sequence records, maps, and related databases.

• 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. Accession numbers have the format of two letters, an underscore bar, and six digits, for example, NC_123456, NT_123456, NM_123456, NP_123456 (more info about accession numbers and access).

• UniGene - ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene within the organism from which the sequences were obtained. Additional information about UniGene is provided above.

• HomoloGene - a gene homology tool that compares nucleotide sequences between pairs of organisms, including human, mouse, rat, zebrafish, and fruit fly, in order to identify putative orthologs. Curated orthologs are incorporated from a variety of sources via Entrez Gene.

• BLAST against the draft human genome sequence - Compare your nucleotide or protein query sequence to the working draft sequence of the human genome, its mRNA and protein products, or the other data sets described below. The genome sequence been assembled from GenBank sequence records (primarily HTGs) using the process described in NCBI Contig Assembly and Annotation Process. The contigs assembled by this process have been given NT_* accession numbers as part of the RefSeq project (described above).

  A variety of database choices are provided on the Human Genome BLAST page.

• Clone Maps - various clone maps for human have been included in the Map Viewer, described below. The document that describes the various maps available for human includes a section listing the maps that contain clone information. To select those maps for display, use the Maps&Options dialog box when viewing any human chromosome. (Several other organisms accessible through the Map Viewer are represented by maps that contain clone information. The organism-specific "data and search tips" files provide additional detail about the maps available for each organism.)

• Clone Registry - a database used by participating human genome sequencing centers and mouse genome sequencing centers to record which clones have been selected for sequencing, which are currently in the pipeline, and which are finished and represented by sequence entries in GenBank. Includes BACs, PACs, cosmids, fosmids. Uses standardized clone names that represents a clone's microtitre plate address (plate number, row, and column) prefixed by a library abbreviation, to produce unique names. Includes clone ordering information.

• Human BAC Resource - A cytogenetic resource of large-insert, FISH-mapped clones containing sequence-tagged sites. Will help integrate cytogenetic, radiation-hybrid, linkage, and sequence maps of the human genome. Includes links to clone distributors.

• Mammalian Gene Collection (MGC) - The NIH Mammalian Gene Collection (MGC) is a trans-NIH initiative that seeks to identify and sequence a representative full open reading frame (FL-ORF) clone for each human, mouse, and rat gene. The MGC project entails the production of cDNA libraries and sequences, database and repository development, as well as the support of research for improved library construction, sequencing, and analytic technologies. All the resources generated by the MGC are publicly accessible to the biomedical research community.

Clone Information for Other (Non-human) Organisms - Some organisms have additional clone information resources. For example, the resources available for the mouse genome include several items mentioned above, plus a CloneFinder, described below. In addition, many records in dbEST (described above) include information about clone sources such as the I.M.A.G.E. consortium.

• Entrez Genome - links to the human chromosome views in the Map Viewer (details below). Entrez Genome also includes a view of the human mitochondrion (accessible under eukaryotic organelles), which can be viewed in its entirety or explored in progressively greater detail (additional information about Entrez Genome above).

• Map Viewer - integrated views of chromosome maps - The Map Viewer is a software component of Entrez Genome that displays one or more maps which have been aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. For human, the Map Viewer includes >20 sequence, cytogenetic, genetic linkage, radiation hybrid, and other maps.  (When viewing a chromosome, use the "Maps & Options" dialog box to display the map(s) of interest.)   The sequence maps are based on the contigs built from the draft and finished sequence data generated by the Human Genome Project. A list of available human maps and their descriptions is provided. The Map Viewer help document provides general information on how to use that tool. Information about the NCBI Contig Assembly and Annotation Process is also available.

• GeneMap'99 - physical map of >35,000 human gene-based markers, constructed by the International Radiation Hybrid Mapping Consortium using a consistent set of RH reagents and methodologies. Provides a framework for accelerated sequencing efforts by highlighting key landmarks (gene-rich regions) of the chromosomes, and represents the cooperative efforts of more than one hundred scientists throughout the world.
  Note: The GeneMap'99 data have also been included in the Map Viewer, described above. When viewing a chromosome, use the "Maps & Options" dialog box to select the map(s) of interest.

• NCBI RH Map - NCBI Integrated Radiation Hybrid Map contains 23,723 markers from both the G3 and GB4 RH panels of GeneMap'99. Those markers were mapped with respect to 1084 framework markers (a subset of markers common to the G3 and GB4 panels). All markers from both panels were interpolated onto the GB4 scale. The article by R. Agarwala et al. provides detail about the integration strategy, as well as the methods used to evaluate the quality of the integrated map.
  Note: The NCBI RH Map data have also been included in the Map Viewer, described above. When viewing a chromosome, use the "Maps & Options" dialog box to select the map(s) of interest.

• Mitelman Database of Chromosome Aberrations in Cancer - genome-wide map of chromosomal breakpoints in human cancer, by Drs. Mitelman, Mertens, and Johansson (eds), http://cgap.nci.nih.gov/Chromosomes/Mitelman. This resource is associated with the Cancer Genome Anatomy Project (CGAP).
  Note: The Mitelman data have also been included in the Map Viewer, described above. When viewing a chromosome, use the "Maps & Options" dialog box to select the map(s) of interest.

• OMIM Gene Map - cytogenetic locations of genes that have been reported in the literature and determined by a variety of mapping methods. Can be searched by gene symbol or cytogenetic chromosomal location. Accessible from the OMIM page (described above).
  Note: The OMIM Gene Map data have also been included in the Genes_Cytogenetic Map of the Map Viewer (described above). When viewing a chromosome, use the "Maps & Options" dialog box to select the map(s) of interest.

• OMIM Morbid Map - alphabetical listing of diseases and corresponding cytogenetic map locations, with links to OMIM entries. Accessible from the OMIM page (described above).
  Note: The OMIM Morbid Map data have also been included in the Map Viewer, described above. When viewing a chromosome, use the "Maps & Options" dialog box to select the map(s) of interest.

• Human-Mouse Homology Maps - a table comparing genes in homologous segments of DNA from human and mouse, sorted by position in each genome. Computed by integrating orthologs identified at The Jackson Laboratory with putative orthologs identified by sequence homology. The original maps by M. F. Seldin of the University of California at Davis are also available.

• dbSTS - Database of Sequence Tagged Sites - short (about 200-500 bp) genomic sequences that are thought to be operationally unique in a genome, and therefore define a specific position on the physical map.

• UniSTS - a unified, non-redundant view of sequence tagged sites (STSs). UniSTS integrates marker and mapping data from a variety of public resources. If two or more markers have different names but the same primer pair, a single STS record is presented for the primer pair and all the marker names are shown. Each UniSTS record displays the primer sequences, product size, mapping information, and cross references to Entrez Gene, dbSNP, RHdb, GDB, MGD, and the Map Viewer. The marker report also lists GenBank and RefSeq records that contain the primer sequences, as determined by Electronic PCR (e-PCR). Data sources include dbSTS, RHdb, GDB, various human maps (Genethon genetic map, Marshfield genetic map, Whitehead RH map, Whitehead YAC map, Stanford RH map, NHGRI chr 7 physical map, WashU chrX physical map), various mouse maps (Whitehead RH map, Whitehead YAC map, Jackson laboratory's MGD map).

• e-PCR (Electronic PCR) - find putative map location of a query sequence. Computational procedure for finding sequence tagged sites in DNA sequences. (See additional information in the Tools/Nucleotide Sequence Analysis Section.)

• GeneMap'99 - physical map of >35,000 human gene-based markers, constructed by the International Radiation Hybrid Mapping Consortium using a consistent set of RH reagents and methodologies. Provides a framework for accelerated sequencing efforts by highlighting key landmarks (gene-rich regions) of the chromosomes, and represents the cooperative efforts of more than one hundred scientists throughout the world.
  Note: The GeneMap'99 data have also been included in the Map Viewer, described above. When viewing a chromosome, use the "Maps & Options" dialog box to select the map(s) of interest.

• Map Viewer - graphical views of STS markers placed on a variety of maps, including sequence, genetic linkage, and radiation hybrid maps. (See additional information about Map Viewer, above.)

• Rl2pl4tg - cytogenetic locations of genes that have been reported in the literature and determined by a variety of mapping methods. Can be searched by gene symbol or cytogenetic chromosomal location. Accessible from the OMIM page (see Genes, above).
  Note: The OMIM Gene Map data have also been included in the Genes_Cytogenetic Map of the Map Viewer (described above). When viewing a chromosome, use the "Maps & Options" dialog box to select the map(s) of interest.

• Human BAC Resource - A cytogenetic resource of large-insert, FISH-mapped clones containing sequence-tagged sites. Will help integrate cytogenetic, radiation-hybrid, linkage, and sequence maps of the human genome. Includes links to clone distributors.

• Cancer Chromosomes - An Entrez database that integrates data from three sources: the NCI/NCBI SKY/M-FISH & CGH Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Aberrations in Cancer. Provides the ability to search for cytogenetic, clinical, and/or reference information.

• SKY/M-FISH & CGH Database - The NCI and NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic Hybridization (CGH), which are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mouse chromosome in a different color, facilitating the identification of chromosomal aberrations; CGH can be used to generate a map of DNA copy number changes in tumor genomes. Collaborative project with the National Cancer Institute.  (data submission instructions...)

• Mitelman Database of Chromosome Aberrations in Cancer - genome-wide map of chromosomal breakpoints in human cancer, by Drs. Mitelman, Mertens, and Johansson (eds), http://cgap.nci.nih.gov/Chromosomes/Mitelman. This resource is associated with the Cancer Genome Anatomy Project (CGAP).
  Note: The Mitelman data have also been included in the Map Viewer, described above. When viewing a chromosome, use the "Maps & Options" dialog box to select the map(s) of interest.

• Gene Expression Omnibus (GEO) - a gene expression and hybridization array data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval. GEO was the first fully public high-throughput gene expression data repository, and became operational in July 2000. Many types of gene expression data from platforms such as spotted microarray (microarray), high-density oligonucleotide array (HDA), hybridization filter (filter) and serial analysis of gene expression (SAGE) data, are accepted, accessioned, and archived as a public data set. GEO data can be accessed through several search and browsing tools on the GEO home page, Entrez (via Entrez GEO Profiles and Entrez GDS (GEO DataSets)), and the FTP site. The Tools/Gene Expression section of this file provides information about data visualization and exploration capabilities available in GEO.

• 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. Collaboration among the National Cancer Institute, the NCBI, and numerous research labs. Additional information about CGAP is provided in the Tools/Gene Expression section of this file. Related resources are described in the Human Genome/Cancer Research section.

• SAGEmap - Serial Analysis of Gene Expression, or SAGE, is an experimental technique designed to quantitatively measure gene expression. SAGEmap is an online tool to compare computed gene expression profiles between SAGE libraries generated by the Cancer Genome Anatomy Project (CGAP, described under human genome/cancer research) and submitted by others through the Gene Expression Omnibus (GEO, described under molecular databases/gene expression). SAGEmap also includes a comprehensive analysis of SAGE tags in human GenBank records, in which a UniGene identifier is assigned to each human sequence that contains a SAGE tag. Data can be retrieved by tag, by sequence, by UniGene cluster ID and by library name. When retrieving data by sequence or UniGene cluster ID, follow a SAGE tag's hotlink to find out its expression level in different SAGE libraries, and how it is represented in the rest of the sequences in GenBank. Retrieving data by library name takes one to GEO, where all SAGEmap data has been stored by library. Analytical tools include xProfiler, which compares gene expression between SAGE libraries of your choice as well as uploaded data. More information about the additional analytical capabilities of the SAGEmap resource is provided in the tools/gene expression section of this file.

• UniGene DDD - Digital Differential Display - an online tool to compare computed gene expression profiles between selected cDNA libraries. Using a statistical test, genes whose expression levels differ significantly from one tissue to the next are identified and shown to the user. Additional information about UniGene is above.

• dbSNP - Database of Single Nucleotide Polymorphisms - NCBI database of single nucleotide polymorphisms, microsatellites, and small-scale insertions and deletions. dbSNP contains population-specific frequency and genotype data, experimental conditions, molecular context, and mapping information for both neutral polymorphisms and clinical mutations.

• OMIM - Online Mendelian Inheritance in Man - allelic variants in ~900 (9%) of OMIM records. To view a list of those OMIM records, use the OMIM Limits page in Entrez and check the box for "Allelic Variants" under the section titled "Only records with." (For more information about OMIM, see Genes, above.)

• Locus Specific Mutation Databases - links to numerous external mutation databases are provided on the OMIM allied resources page and from related OMIM entries. When an individual OMIM entry contains links to locus-specific mutation databases, the links are shown under the "LinkOut" header in the blue sidebar. (The LinkOut header appears only in entries that have links to resources outside of the Entrez system.)

• Genes and Disease - introduction to the relationship between genetic factors and human disease. Summary information for ~60 genetic diseases with links to related databases and organizations.

• Mitelman Database of Chromosome Aberrations in Cancer - genome-wide map of chromosomal breakpoints in human cancer, by Drs. Mitelman, Mertens, and Johansson (eds), http://cgap.nci.nih.gov/Chromosomes/Mitelman. This resource is associated with the Cancer Genome Anatomy Project (CGAP).

• OMIM - Online Mendelian Inheritance in Man - continuously updated catalog of human genes and genetic disorders, with links to associated literature references, sequence records, maps, and related databases.

• OMIM Morbid Map - alphabetical listing of diseases and corresponding cytogenetic map locations, with links to OMIM entries. Accessible from OMIM page (see Genes).

• Cancer Chromosomes - An Entrez database that integrates data from three sources: the NCI/NCBI SKY/M-FISH & CGH Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Aberrations in Cancer. Provides the ability to search for cytogenetic, clinical, and/or reference information.

• CCAP - Cancer Chromosome Aberration Project - designed to expedite the definition and detailed characterization of the distinct chromosomal alterations that are associated with malignant transformation. Collaboration among the National Cancer Institute, the NCBI, and numerous research labs.

• 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. Collaboration among the National Cancer Institute, the NCBI, and numerous research labs. Additional information about CGAP is provided in the Tools/Gene Expression section of this file.

• Mitelman Database of Chromosome Aberrations in Cancer - genome-wide map of chromosomal breakpoints in human cancer, by Drs. Mitelman, Mertens, and Johansson (eds), http://cgap.nci.nih.gov/Chromosomes/Mitelman. This resource is associated with the Cancer Genome Anatomy Project (CGAP).

• SKY/M-FISH & CGH Database - The NCI and NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic Hybridization (CGH), which are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mouse chromosome in a different color, facilitating the identification of chromosomal aberrations; CGH can be used to generate a map of DNA copy number changes in tumor genomes. Collaborative project with the National Cancer Institute.  (data submission instructions...)

• SAGE Analysis - differential expression of SAGE tags in cancer libraries. (See additional information about SAGEmap, below.)

• Human chromosome data - the ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ directory contains one folder for each chromosome, which includes genomic contigs (NT_* records) built from finished and unfinished sequence data. The contigs are available in various formats, described below. The contig assembly and annotation process is described in a separate document.

  hs_chr*.asn	ASN.1 format (description above)
  hs_chr*.fa.gz	FASTA format (description above)
  hs_chr*.gbk.gz	GenBank flat file format (annotations currently include STS markers; known and predicted genes will be added in coming months)
  hs_chr*.gbs	GenBank summary format (this format does not contain sequence data, but instead contains a "CONTIG" field, showing how the contig is assembled from individual GenBank accessions)

  Data from the Map Viewer (described above), is available in the ftp://ftp.ncbi.nih .gov /genomes/H_sapiens/maps/mapview/ subdirectory.

Guide,   Chromosomes,   Sequences,   Genes,   Clones,   Maps and Mapped Markers,   Cytogenetics,   BLAST,   FTP

• Mouse Genome Resources Guide - brings together information on diverse mouse-related resources from multiple centers: sequence, mapping, and clone information as well as pointers to strain and mutant resources.

• Mouse Genome Sequencing - sequencing progress of the Mouse Genome Project; high-throughput genomic sequence contigs assembled from finished (phase 3) data; view by chromosome number, size and physical position; download sequence data by contig or by chromosome; BLAST against contigs.

• Map Viewer - integrated chromosome maps - The Map Viewer is a software component of Entrez Genome that displays one or more maps which have been aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. The maps that are currently available for Mus musculus are described in the Mus musculus data and search tips document. The Map Viewer help document provides general information on how to use that tool.

• Mouse Genome Sequencing - sequencing progress of the Mouse Genome Project; high-throughput genomic sequence contigs assembled from finished (phase 3) data; view by chromosome number, size and physical position; download sequence data by contig or by chromosome; BLAST against contigs.

• Entrez - includes sequence data from >160,000 species; use the organism field to limit searches to mouse records. See additional information about Entrez above, and Batch Entrez, below.

• Entrez Gene - a gene-based view of the data from a wide range of genomes, including mouse. It supplies key connections in the nexus of map, sequence, expression, structure, functional, and homology data. More information about Entrez Gene is provided above, in the Molecular Databases/Genes section.

• UniGene - ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene within the organism from which the sequences were obtained. Additional information about UniGene is provided above.

• HomoloGene - a gene homology tool that compares nucleotide sequences between pairs of organisms, including human, mouse, rat, zebrafish, and fruit fly, in order to identify putative orthologs. Curated orthologs are incorporated from a variety of sources via Entrez Gene.

• CloneRegistry - a database used by participating human genome sequencing centers and mouse genome sequencing centers to record which clones have been selected for sequencing, which are currently in the pipeline, and which are finished and represented by sequence entries in GenBank. Includes BACs, PACs, cosmids, fosmids. Uses standardized clone names that represents a clone's microtitre plate address (plate number, row, and column) prefixed by a library abbreviation, to produce unique names. Includes clone ordering information.

• Mammalian Gene Collection (MGC) - The NIH Mammalian Gene Collection (MGC) is a trans-NIH initiative that seeks to identify and sequence a representative full open reading frame (FL-ORF) clone for each human, mouse, and rat gene. Additional information is provided above.

• CloneFinder - allow users to identify clones that contain an object, or that are contained within a particular genomic region. Clone placement is based on the alignment of BAC end sequences (BES) to the current genome assembly. Currently, CloneFinder is available for mouse only.

• Map Viewer - integrated chromosome maps - The Map Viewer is a software component of Entrez Genome that displays one or more maps which have been aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. The maps that are currently available for Mus musculus are described in the Mus musculus data and search tips document. The Map Viewer help document provides general information on how to use that tool.

• Human-Mouse Homology Maps - a table comparing genes in homologous segments of DNA from human and mouse, sorted by position in each genome. Computed by integrating orthologs identified at The Jackson Laboratory with putative orthologs identified by sequence homology. The original maps by M. F. Seldin of the University of California at Davis are also available.

• UniSTS - a unified, non-redundant view of sequence tagged sites (STSs). UniSTS integrates marker and mapping data from a variety of public resources. If two or more markers have different names but the same primer pair, a single STS record is presented for the primer pair and all the marker names are shown. Each UniSTS record displays the primer sequences, product size, mapping information, and cross references to Entrez Gene, dbSNP, RHdb, GDB, MGD, and the Map Viewer. The marker report also lists GenBank and RefSeq records that contain the primer sequences, as determined by Electronic PCR (e-PCR). Data sources include dbSTS, RHdb, GDB, various human maps (Genethon genetic map, Marshfield genetic map, Whitehead RH map, Whitehead YAC map, Stanford RH map, NHGRI chr 7 physical map, WashU chrX physical map), various mouse maps (Whitehead RH map, Whitehead YAC map, Jackson laboratory's MGD map).

• SKY/M-FISH & CGH Database - The NCI and NCBI SKY/M-FISH and CGH Database is a repository of publicly submitted data from Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH), and Comparative Genomic Hybridization (CGH), which are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mouse chromosome in a different color, facilitating the identification of chromosomal aberrations; CGH can be used to generate a map of DNA copy number changes in tumor genomes. Collaborative project with the National Cancer Institute.  (data submission instructions...)

• BLAST against the mouse genome -   Nucleotide or protein query sequences can be used. A variety of database choices are provided.

• Mouse chromosome data - the ftp://ftp.ncbi.nih.gov/genomes/M_musculus/ directory contains one folder for each chromosome, which includes genomic contigs (NT_* records) built from finished sequence data. The contigs are available in various formats:

  mm_chr*.asn	ASN.1 format (description above)
  mm_chr*.fa.gz	FASTA format (description above)
  mm_chr*.gbk.gz	GenBank flat file format (annotations currently include STS markers; known and predicted genes will be added in coming months)
  mm_chr*.gbs	GenBank summary format (this format does not contain sequence data, but instead contains a "CONTIG" field, showing how the contig is assembled from individual GenBank accessions)

  See additional information about the genomes FTP directories, below

• select Drosophila genome as the target database when using the nucleotide BLAST, protein BLAST, or translated BLAST search pages.  Or,
• check the box for Drosophila melanogaster in the list of organisms on the BLAST with Eukaryotic genomes page.

• check the box for Saccharomyces cerevisiae and/or Schizosaccharomyces pombe in the list of organisms on the BLAST with Eukaryotic genomes page.   OR
• select yeast as the target database when using the nucleotide BLAST, protein BLAST, or translated BLAST search pages; this searches only Saccharomyces cerevisiae data, however.

• The malaria genome sequence (both Plasmodium yoelii shotgun sequences and Plasmodium falciparum complete finished sequence) as submitted to GenBank is available at the Entrez Genome Malaria BLAST page.
• Prior release and unsubmitted sequence data to GenBank is available from the NCBI Malaria Genetics & Genomics Custom BLAST page.

• Electronic PCR (e-PCR) program for finding STSs in DNA sequences, Malaria Packaging Version - Standalone Program. (See additional information in the Tools/Nucleotide Sequence Analysis Section.)
• download completed chromosome sequence data

• complete bacterial genomes as submitted to GenBank.
• complete bacterial genomes from the RefSeq database (described above).

(See additional note in the FTP section, below, about the two different FTP directories)

Text Term Searching (Entrez),   Sequence Similarity Searching (BLAST),   Nucleotide Sequence Analysis,   Protein Sequence Analysis and Proteomics,   3-D Structure Display and Similarity Searching,   Genome Analysis,   Gene Expression

• Two unique features of Entrez are:
1. pre-computed similarity searches for each database record, identifying the related records ("neighbors") within that database. The algorithm used to identify related records depends upon the database.
2. links from a record in one database to associated records in the other Entrez databases, providing integrated access across the various databases. For exmaple, if a MEDLINE record cites a GenBank nucleotide sequence record, which in turn is linked to a protein translation, there will be a link between those three records. The Entrez Data Model illustrates the links that exist among the various Entrez Databases.
• Entrez can be searched with a wide variety of text terms such as author name, journal name, gene or protein name, organism, unique identifier (e.g., accession number, sequence ID, PubMed ID), and other terms, depending on the database being searched.
• The help document provides more information about the databases available in Entrez as well as search tips. External resources can be linked to Entrez records using the new Linkout service (described below). Entrez also allows users to store search strategies and select a customized subset of LinkOut links through the NCBI My NCBI service (described below).

• Citation Matcher for single articles

• Batch Citation Matcher for many articles

• MegaBLAST against the Trace Archives - compare nucleotide sequence data against the raw data underlying all of the sequence generated by various genome projects. Additional information about the Trace Archive is above.

• Discontiguous MegaBLAST against the Trace Archives - compare diverged nucleotide sequences, especially sequences from different organisms (which have alignments with low degree of identity) against the raw data underlying all of the sequence generated by various genome projects. Additional information about the Trace Archive is above, and a separate page provides more about discontiguous MegaBLAST.

• Forward e-PCR - Search STS database with a query sequence. Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that could represent the PCR primers used to generate known STSs.
• Reverse e-PCR - Search sequence database with STS. The main motivation for implementing reverse searching (called Reverse e-PCR) was to make it feasible to search the human genome sequence and other large genomes. The new version of e-PCR provides a search mode using a query sequence against a sequence database.

• Gene Library Summarizer (GLS) - Tool that finds all the genes in a specific cDNA library or group of libraries.
• cDNA Expression Profiler (xProfiler) - an online tool to compare computed gene expression profiles between selected cDNA libraries.
• Differential Gene Expression Displayer (DGED) - distinguishes statistical differences in gene expression between two pools of libraries.

News,   Books,   Glossaries,   Tutorials,   Courses,   Additional Resources

• Human Genome Build Glossary - accompanies the document that describes the NCBI Genomic Sequence Assembly and Annotation Process.

• Query Tutorial - formulating a BLAST query; entering sequence data; beginners welcome!

• BLAST Tutorial - setting up a protein query; parameters - how and why; interpreting BLAST output

• BLAST Guide - printable; setting-up a query; deciphering results; post-BLAST analysis

• PSI-BLAST Tutorial - when to use PSI-BLAST; understanding iterations; interpreting PSI-BLAST output

• More Information - principles of similarity searching; rules of thumb; glossary of terms; references.

• Exploring 3D Molecular Structures Using NCBI Tools - a companion to the Field Guide that focuses specifically on effectively using the NCBI databases, search services, and analysis tools to mine 3D macromolecular structure data. The course includes a 60-minute lecture plus a 90-minute computer workshop. It is offered by NCBI staff at various universities throughout the country can be requested along with a Field Guide or separately.

• Introduction to Molecular Biology Information Resources - a three-day Medical Library Association (MLA) CE Course designed for librarians who have little or no experience with molecular biology databases and search systems, and who handle occasional questions about those resources at the reference desk. Course format combines lecture, demonstration, and hands-on experience and is approved by MLA for 20 CE hours.

• NCBI Advanced Workshop for Bioinformatics Information Specialists - a five-day workshop designed for library staff with a science background who have full-time bioinformatics support positions. This includes bioinformatics librarians as well as scientists who have been hired by libraries to establish training and user support programs. Applicants must already have some experience with molecular biology databases and software programs. Course format combines lecture, demonstration, and hands-on experience and is approved by the Medical Library Association (MLA) for 40 CE hours.

• NCBI PowerScripting

• Programming with NCBI BLAST

• NCBI 4-Pack: Practical Web-based Analysis

• GenBank flat file format - see sample GenBank record and detailed description in GenBank release notes; download most recent full release (described above) and daily cumulative or non-cumulative update files

• ASN.1 format - Abstract Syntax Notation 1, an International Standards Organization (ISO) data representation format; download most recent full release (described above) and daily cumulative or non-cumulative update files.  (more on ASN.1)

• FASTA format - definition line followed by sequence data only (example). The FASTA formatted data are available in the BLAST databases directory of the FTP site. A readme file in that directory provides descriptions of the available data sets, such as nt.Z (daily updated non-redundant BLAST nucleotide database, contains GenBank+EMBL+DDBJ+PDB sequences, but no EST, STS, GSS, or HTGS sequences), nr.Z (daily updated non-redundant proteins), est.Z, gss.Z, htg.Z, sts.Z, and others.

• ftp://ftp.ncbi.nih.gov/genomes/ - designed to contain genomes assembled and/or curated at NCBI. These genomes are part of the RefSeq database, described above.
• ftp://ftp.ncbi.nih.gov/genbank/ge nome s/ - designed to contain complete genomes submitted in their entirety to GenBank

Note: In some cases, an organism might be listed in both directories. This can happen for several reasons: (1) there are two versions of the genome are available - one in GenBank, and one in RefSeq; or (2) the organism's data was assembled at NCBI and was available from the "/genbank/genomes/" directory before the new "/genomes/" directory was set up. In the latter case, the data now exists in the new "/genomes/" directory, but a symbolic link was preserved in the original directory to facilitate user access.

• BLAST Stand-Alone Program - a set of executables which are run by command line. Binaries are provided for IRIX 6.2, Solaris 2.6, DEC OSF1 (ver. 4.0d), LINUX, and Win32 systems. Please read the README for more information. There is also some information on setting up Standalone BLAST at the NHGRI site at http://genome.nhgri.n ih.g ov/blastall/blast_install/.

• BLAST Web Server Program - allows you to set up your own in-house version of the NCBI BLAST web pages on a UNIX web server. You can set up the program to search your own custom databases or downloaded copies of the NCBI databases. This server is not intended to handle the large loads which may exist in public service settings. A Read me file provides more information.

• Network BLAST - a TCP/IP-based client-server version of WWW Gapped BLAST (2.0). Makes a direct connection with the NCBI databases over the Internet to retrieve data. Client software is available for PC, Mac, and Unix. For general information about Gapped BLAST, see above.

NOTE: Preformatted BLAST databases also available for downloading, in addition to the software listed above. A readme file provides database descriptions.

• Sequin - submission software program for one or many submissions, long sequences, complete genomes, alignments, population/ phylogenetic/ mutation studies. Can be used as a stand-alone application or in a TCP/IP-based "network aware" mode, with links to other NCBI resources and software such as Entrez.

• Network Entrez - a TCP/IP-based client-server version of WWW Entrez. Makes a direct connection with the NCBI databases over the Internet to retrieve data. Client software is available for PC, Mac, and Unix. For general information about Entrez, see above.

• Network BLAST - see description above.