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NCBI Nucleotide Database Edit

The Nucleotide database is used for genome, gene, and transcript sequence data. It provides information from multiple sources for the main purpose of biomedical research through access to Entrez. These sources include GenBank, RefSeq, TPA and PDB. Although there are other databases that contain nucleotide sequences, the Nucleotide database allows the researcher to use "general text queries" that will give the best results. Updates to the Nucleotide database are made every day to further expand the worlds knowledge of sequencing. This is done as a collaborative effort by DDBJ, EMBL, and GenBank.

History Edit

The Entrez Nucleotide database is through the NCBI, which is under the wing of the United States Department of Health and Human Services. It began in 199,1 where the Entrez system was on a CD (Compact-Disc). A few years later when the internet started to take stride, Entrez became available for the world.

Usage Edit

This database has the capability of search settings where the researcher can choose limits to what the search engine retrieves. Under the Tool bar at the home page, the user has the option to set these limits. As seen in Figure 1, the limits include Publication dates, Field tags, database source, Gene location, modifications, Segmented sequences, and Molecule. This means that the user can select specific organisms to search for, the database that he/she wants information drawn from, and even the type of Molecule being searched for such as genomic DNA or RNA. There are many options as well to limit the search to get desired information. As seen in Figure 2, a simple search for Staphylococcus aureus (Strain MRSA252) retrieves several hundred thousand publications with nucleotide sequences.

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Figure 2

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Figure 1

Once the desired page has been found, clicking on the link "FASTA" below the heading provides the entire sequenced genome. On the right side of the page, the NCBI provides services such as the ability to run BLAST, pick primers, and highlight sequence features (Figure 3).

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Figure 3

In this database there are database identifiers called Accession Numbers that will allow the system to find a full record of a sequence. Understanding how to use these numbers with this database as well as GenBank, DDBJ and EMBL can be accessed here.

Applications Edit

The NCBI Nucleotide Database, as previously mentioned, is linked to other sources such as GenBank. The fact that these sources are linked provide researchers with a seemingly endless amount of Single Nucleotide Polymorphisms (SNP's) that can be applied to why diseases are caused through the deepest level of analysis. Looking at genetic sequences to determine the functionality of the gene is crucial to the advancement of human knowledge. The idea that the nucleotide database provides billions of different nucleotides gives researchers an endless amount of possibilities.

References Edit

Entrez Sequencing Quick Start

Entrez: Wikipedia

Nucleotide Database

GenBank

Accession Numbers via NCBI

DDBJ

EMBL