<< Chapter < Page Chapter >> Page >
This module is an introduction to performing searches of the NCBI databases using Entrez, the NCBI web-based search and retrieval tool for integrated search results from multiple databases.

Entrez (1) is a search and retrieval tool developed by NCBI that is capable of searching multiple NCBI databases with just one query. Entrez returns search results that can include a combination of many types of data on the query, such as nucleotide sequences, protein sequences, macromolecular structures, and related articles in the literature. Prior to the creation of Entrez, an individual might have to place one query to a nucleotide database to find a nucleotide sequence, submit another query to a structural database to find the published structure of the gene product, and submit a final query to a literature database to find citations for journal articles on the query topic. NCBI recognized the time and effort that could be saved by a tool that could cross-link these databases and integrate all information related to a given query subject into one report.View the Entrez Database page . This module contains a few problem questions, for use in a computer lab setting. The lab instructor may require that yousupply answers to these questions as an indication that you have completed the module.

The Entrez Nucleotides database includes sequences from GenBank, RefSeq, and PDB. GenBank is the National Institutes of Health (NIH) genetic sequencedatabase. GenBank, the DNA DataBank of Japan (DDBJ) and the European Molecular Biology Laboratory (EMBL) comprise the International Nucleotide SequenceDatabase Collaboration. These three organizations exchange data on a daily basis. The number of bases in the Entrez Nucleotides database currently growsat an exponential rate. Click on the Nucleotide link listed under the heading "Nucleotide Databases".

What is the number of bases stored in the Entrez nucleotide database, as of the last report?

Got questions? Get instant answers now!

Use the back arrow of the browser to return to the Entrez Database web page. Locate the MMDB (Molecular Modeling DataBase), one of NCBI's structure databases and clickon the link to read about it. MMDB is a subset of three-dimensional structures obtained from the ProteinData Bank (PDB), excluding theoretical models. While the protein databases contain protein sequences, the structural database contains coordinate files (PDB files) of biological molecules with solved (known) structures.Click on the arrow next to the search box at the top of the web page and view the list of databases for selection.The literature database is accessed through PubMed, which encompasses the National Library of Medicine'sjournals database, MEDLINE, as well as providing some additional online services. MEDLINE is a collection of medical and life science journalcitations that includes articles dating back to the mid-1960's.Entrez allows access to information such as nucleotide and protein sequencesorganized by species in the NCBI taxonomy database, also found on the selection list. The connectivity of the databases available on the selection list are indicated by the diagram on the Entrez Database web page . Click on the diagram to access a Flash model of Entrez database connectivity. As long as the browser has a Flash plug-in, placing the mouse over one of the nodes representing a database will highlight its connectivity.Try this on the node labeled "Protein". Actually clicking on the node will forward the user to the database home page.

Questions & Answers

what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
How we are making nano material?
what is a peer
What is meant by 'nano scale'?
What is STMs full form?
scanning tunneling microscope
how nano science is used for hydrophobicity
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
what is differents between GO and RGO?
what is simplest way to understand the applications of nano robots used to detect the cancer affected cell of human body.? How this robot is carried to required site of body cell.? what will be the carrier material and how can be detected that correct delivery of drug is done Rafiq
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
The nanotechnology is as new science, to scale nanometric
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
what school?
biomolecules are e building blocks of every organics and inorganic materials.
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
sciencedirect big data base
Introduction about quantum dots in nanotechnology
Praveena Reply
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
Damian Reply
absolutely yes
how to know photocatalytic properties of tio2 nanoparticles...what to do now
Akash Reply
it is a goid question and i want to know the answer as well
characteristics of micro business
for teaching engĺish at school how nano technology help us
How can I make nanorobot?
Do somebody tell me a best nano engineering book for beginners?
s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
how can I make nanorobot?
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
what is the actual application of fullerenes nowadays?
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
Got questions? Join the online conversation and get instant answers!
Jobilize.com Reply

Get the best Algebra and trigonometry course in your pocket!

Source:  OpenStax, Bios 533 bioinformatics. OpenStax CNX. Sep 24, 2008 Download for free at http://cnx.org/content/col10152/1.16
Google Play and the Google Play logo are trademarks of Google Inc.

Notification Switch

Would you like to follow the 'Bios 533 bioinformatics' conversation and receive update notifications?