Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources

BIOINFORMATICS

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological information generated by the scientific community. This deluge of genomic information has, in turn, led to an absolute requirement for computerized databases to store, organize, and index the data and for specialized tools to view and analyze the data.

What Is a Biological Database?

A biological database is a large, organized body of persistent data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system. A simple database might be a single file containing many records, each of which includes the same set of information. For example, a record associated with a nucleotide sequence database typically contains information such as contact name, the input sequence with a description of the type of molecule, the scientific name of the source organism from which it was isolated, and often, literature citations associated with the sequence.

At NCBI, many of our databases are linked through a unique search and retrieval system, called Entrez. Entrez (pronounced ahn' tray) allows a user to not only access and retrieve specific information from a single database but to access integrated information from many NCBI databases. For example, the Entrez Protein database is cross-linked to the Entrez Taxonomy database. This allows a researcher to find taxonomic information (taxonomy is a division of the natural sciences that deals with the classification of animals and plants) for the species from which a protein sequence was derived.

What Is Bioinformatics?

Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. At the beginning of the "genomic revolution", a bioinformatics concern was the creation and maintenance of a database to store biological information, such as nucleotide and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could both access existing data as well as submit new or revised data.

Ultimately, however, all of this information must be combined to form a comprehensive picture of normal cellular activities so that researchers may study how these activities are altered in different disease states. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include:

• the development and implementation of tools that enable efficient access to, and use and management of, various types of information



• the development of new algorithms (mathematical formulas) and statistics with which to assess relationships among members of large data sets, such as methods to locate a gene within a sequence, predict protein structure and/or function, and cluster protein sequences into families of related sequences

Why Is Bioinformatics So Important?

Evolutionary Biology

New insight into the molecular basis of a disease may come from investigating the function of homologs of a disease gene in model organisms. In this case, homology refers to two genes sharing a common evolutionary history. Scientists also use the term homology, or homologous, to simply mean similar, regardless of the evolutionary relationship.

Equally exciting is the potential for uncovering evolutionary relationships and patterns between different forms of life. With the aid of nucleotide and protein sequences, it should be possible to find the ancestral ties between different organisms. Thus far, experience has taught us that closely related organisms have similar sequences and that more distantly related organisms have more dissimilar sequences. Proteins that show a significant sequence conservation, indicating a clear evolutionary relationship, are said to be from the same protein family. By studying protein folds (distinct protein building blocks) and families, scientists are able to reconstruct the evolutionary relationship between two species and to estimate the time of divergence between two organisms since they last shared a common ancestor.

Protein Modeling

The process of evolution has resulted in the production of DNA sequences that encode proteins with specific functions. In the absence of a protein structure that has been determined by X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, researchers can try to predict the three-dimensional structure using protein or molecular modeling. This method uses experimentally determined protein structures (templates) to predict the structure of another protein that has a similar amino acid sequence (target).

Although molecular modeling may not be as accurate at determining a protein's structure as experimental methods, it is still extremely helpful in proposing and testing various biological hypotheses. Molecular modeling also provides a starting point for researchers wishing to confirm a structure through X-ray crystallography and NMR spectroscopy. Because the different genome projects are producing more sequences and because novel protein folds and families are being determined, protein modeling will become an increasingly important tool for scientists working to understand normal and disease-related processes in living organisms.

Genome Mapping

Genomic maps serve as a scaffold for orienting sequence information. A few years ago, a researcher wanting to localize a gene, or nucleotide sequence, was forced to manually map the genomic region of interest, a time-consuming and often painstaking process. Today, thanks to new technologies and the influx of sequence data, a number of high-quality, genome-wide maps are available to the scientific community for use in their research.

Computerized maps make gene hunting faster, cheaper, and more practical for almost any scientist. In a nutshell, scientists would first use a genetic map to assign a gene to a relatively small area of a chromosome. They would then use a physical map to examine the region of interest close up, to determine a gene's precise location. In light of these advances, a researcher's burden has shifted from mapping a genome or genomic region of interest to navigating a vast number of Web sites and databases.

Map Viewer: A Tool for Visualizing Whole Genomes or Single Chromosomes

NCBI's Map Viewer is a tool that allows a user to view an organism's complete genome, integrated maps for each chromosome (when available), and/or sequence data for a genomic region of interest. When using Map Viewer, a researcher has the option of selecting either a "Whole-Genome View" or a "Chromosome or Map View". The Genome View displays a schematic for all of an organism’s chromosomes, whereas the Map View shows one or more detailed maps for a single chromosome. If more than one map exists for a chromosome, Map Viewer allows a display of these maps simultaneously.