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http://www.ebi.ac.uk/ena/

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

Proper citation: European Nucleotide Archive (ENA) (RRID:SCR_006515) Copy   

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http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&BLAST_PROGRAMS=blastx&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome

Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.

Proper citation: BLASTX (RRID:SCR_001653) Copy   

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http://www.ncbi.nlm.nih.gov/SNP/

General database of genetic variations maintained by the NCBI. Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.

Proper citation: dbSNP (RRID:SCR_002338) Copy   

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http://blast.ncbi.nlm.nih.gov/Blast.cgi

Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.

Proper citation: NCBI BLAST (RRID:SCR_004870) Copy   

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http://www.ncbi.nlm.nih.gov/protein

Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

Proper citation: NCBI Protein Database (RRID:SCR_003257) Copy   

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http://www.ncbi.nlm.nih.gov/igblast/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine.

Proper citation: IgBLAST (RRID:SCR_002873) Copy   

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http://www.ncbi.nlm.nih.gov/nucleotide

Database of nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

Proper citation: NCBI Nucleotide (RRID:SCR_004860) Copy   

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https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

Proper citation: Entrez (RRID:SCR_016640) Copy   

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https://www.ncbi.nlm.nih.gov/sites/batchentrez

Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers.

Proper citation: Batch Entrez (RRID:SCR_016634) Copy   

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http://www.ncbi.nlm.nih.gov/Genbank/

NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.

Proper citation: GenBank (RRID:SCR_002760) Copy   

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http://www.ncbi.nlm.nih.gov/popset

Database containing a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. Users may submit a Popset using Sequin.

Proper citation: NCBI Popset (RRID:SCR_005049) Copy   

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http://www.ncbi.nlm.nih.gov/HTGS/

Database of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. It was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. Sequences are prepared for submission by using NCBI's software tools Sequin or tbl2asn. Each center has an FTP directory into which new or updated sequence files are placed. Sequence data in this division are available for BLAST homology searches against either the htgs database or the month database, which includes all new submissions for the prior month. Unfinished HTG sequences containing contigs greater than 2 kb are assigned an accession number and deposited in the HTG division. A typical HTG record might consist of all the first-pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, which together make up more than 2 kb and contain one or more gaps. A single accession number is assigned to this collection of sequences, and each record includes a clear indication of the status (phase 1 or 2) plus a prominent warning that the sequence data are unfinished and may contain errors. The accession number does not change as sequence records are updated; only the most recent version of a HTG record remains in GenBank.

Proper citation: High Throughput Genomic Sequences Division (RRID:SCR_002150) Copy   

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http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch

Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.

Proper citation: BLASTN (RRID:SCR_001598) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html

Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.

Proper citation: BLASTClust (RRID:SCR_016641) Copy   

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http://www.ncbi.nlm.nih.gov/unists

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. Chromosome maps are labeled by name of the originating organism, the map title, total markers, total UniSTSs and links to view maps as well as research documents available through PubMed, another NCBI database. The search functions within UniSTS allow the user to search by gene marker, chromosome, gene symbol and gene description terms to locate markers on specified genes. A representation of the UniSTS datasets is available by ftp. NOTE: All data from this resource have been moved to the Probe database, http://www.ncbi.nlm.nih.gov/probe. You can retrieve all UniSTS records by searching the probe database using the search term unists(properties). (use brackets insead of parenthesis). Additionally, legacy data remain on the NCBI FTP Site in the UniSTS Repository (ftp://ftp.ncbi.nih.gov/pub/ProbeDB/legacy_unists).

Proper citation: UniSTS (RRID:SCR_006843) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/taxonomy/

Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.

Proper citation: NCBI Taxonomy (RRID:SCR_003256) Copy   

•   Source: SciCrunch Registry