Ncbi: national center for biotechnology information

The National Center for Biotechnology Information (NCBI) provides a comprehensive website for biologists that includes biology-related databases, and tools for viewing and analyzing the data inherent in the databases. A division of the National Library of Medicine at the National Institutes of Health, NCBI is theagency responsible for creating automated systems for storing and analyzing the rapidly growing profusion of genetic and molecular data. One of the most difficult challenges faced in the field of bioinformatics is how to store, in an easilyaccessible manner, the overwhelming abundance of new information, including the sequences of entire genomes, the ongoing discoveries of new genes and gene products, and the determinations of their functions and structures. NCBI was establishedas the government's response to the need for more and better information processing methods to deal with this challenge.

View the NCBI home page . A relatively good overview of the tools and databases that can be accessed through NCBI is provided in the list along the left border of the home page.Clicking on the link entitled "About NCBI" produces a second menu containing the topics "A Science Primer", and "Databases and Tools", among others. Click on "A Science Primer" to access general definitions and introductory informationregarding the branches of science included in bioinformatics. Many bioinformatics terms are defined in this section in a clear-cut and basic manner, making this Primer an excellent first resource. From the table at the top of theweb page, click on "Databases and Tools" to yield a listing of accessible information.This web page containing the databases and tools menu is a good choice for those who are inclined toward bookmarking.

The first item under the "Databases and Tools" menu is "Literature Databases". PubMed is the most heavily used of the literature databases and can be used to access MEDLINE biological and medical scientific journal citations dating back toarticles written in the mid-1960's. The second item under the "Databases and Tools"menu is "Entrez Databases". Entrez (1) is a search and retrieval system developed by NCBI that is capable of accessingintegrated information by searching many of the NCBI databases with just one query (instead of searching only one database per query, then having to repeat the query to find information on the same topic from another NCBI database).The NCBI databases that are included in the search when you launch an Entrez query are shown when you click on this link. Look down the list and read the descriptionfor the "Protein sequence database". Notice this database has many sources such as Swiss-Prot, PIR, PRF, PDB, and GenBank, which are all individualbiological databases in their own right, containing different types of data about proteins. The Entrez accessible "Nucleotide sequence database" contains annotatedcollections of publicly available nucleotide sequences, many of which are cDNA and mRNA sequences. The evolution of bioinformatics data mining methodshas been largely driven by the prodigious amount of sequence information collected by scientists in recent years. New sequences of unknown functioncan be compared with sequences of well-characterized genes and proteins. Similarities can be identified between the new, unknown sequences and thewell-characterized sequences, and used to postulate theories regarding function or structure.

Click on "Databases and Tools" from the table at the top of the web page. Selecting the "Tools for Data Mining" topic will show alist of data retrieval tools, including Entrez, mentioned above, and BLAST, the Basic Local Alignment Search Tool (2). Blast is the predominant sequence alignment tool for performing rapid searches of nucleotide and protein sequence databases and detecting local, as well as global,sequence alignments between the query sequence and the database sequences.

This is a brief glimpse at some of the more widely used tools and databases presented by NCBI. As a final exercise, take a moment to select the"Outreach and Education" link from the table. There are two links on this page that may prove helpful at times, "Courses and Tutorials" and "Glossaries". There are tutorialsin the use of Blast, Entrez and Pubmed, among others. Return to these as needed while learning the use of these tools. The Glossaries are particularly usefulbecause bioinformatics has a lot of field-specific lingo and acronyms that can be relatively confusing to decipher.