Bioinformatics or computational biology is the use of mathematical and informational techniques, including statistics , to solve biological problems, usually by creating or using computer programs , mathematical models or both. One of the main areas of bioinformatics isthe data mining and analysis of the data gathered by the various genome projects . Other areas are sequence alignment , protein structure prediction , systemsbiology , protein-protein interactions and virtual evolution . As a summary, the various genome projects produce many long lists of letters and oneof the roles of bioinformatics is to attempt to determine the words, grammar, sentences and ultimately, meaning (functionalsignificance) of those letters.
Since the Epstein-Barr virus was sequenced in 1984 , the DNA sequence of more and more organisms is stored in electronic databases. These data are analyzed todetermine genes that code for proteins , as well as regulatory sequences. A comparisonof genes within a species or between different species can show similarities betweenprotein functions, or relations between species (the use of molecular systematics to construct phylogenetic trees ). With the growing amount of data, it becomes impossible to analyze DNA sequencesmanually. Today, computer programs are used to find similar sequences in the genome ofdozens of organisms, within billions of nucleotides . These programs cancompensate for mutations (exchanged, deleted or inserted bases) in the DNA sequence, in order to identify sequences that arerelated, but not identical. A variant of this sequencealignment is used in the sequencing process itself. The so-called shotgun sequencing (that was used, for example, by Celera Genomics to sequence the human genome ) doesnot give a sequential list of nucleotides, but instead the sequences of thousands of small DNA fragments (each about 600nucleotides long). The ends of these fragments overlap and, aligned in the right way, make up the complete genome. Shotgunsequencing yields sequence data quickly, but the task to re-align the fragments can be quite complicated for larger genomes. Inthe case of the Human Genome Project , it took severalmonths on a supercomputer array to align them correctly. Shotgun sequencing is generally preferred for smaller genomes, such asbacteria, and often used at least partially on organisms with much larger genomes.
Another aspect of bioinformatics in sequence analysis is the automatic search for genes and regulatory sequences within a genome. Not all of the nucleotides within a genome aregenes. Within the genome of higher organisms, large parts of the DNA do not serve any obvious purpose. This so-called junk DNA may, however, contain unrecognized functional elements. Bioinformatics helps tobridge the gap between genome and proteome projects, for example in the use of DNAsequence for protein identification.
Computer scripting languages such as Perl and Python are often used to interface with biological databases and parse output from bioinformatics programs. Communities of bioinformatics programmers have set up free/open source projects such as EMBOSS , BioPerl , BioPython , BioRuby , and BioJava which develop and distribute shared programming tools and objects (as programmodules) that make bioinformatics easier.
Bioinformatics and structural biology
Main article: Protein structureprediction
Protein structure prediction is another important application of bioinformatics. The amino acid sequence of a protein, theso-called primary structure, can be easily determined from the sequence on the gene that codes for it. But, the proteincan only function correctly if it is folded in a very special and individual way (if it has the correct secondary , tertiary and quaternary structure). The prediction of this folding just by looking at the amino acid sequenceis quite difficult. Several methods for computer predictions of protein folding are currently ( as of 2004 ) under development.
One of the key principles in bioinformatics is homology .In the genomic branch of bioinformatics, homology is used to predict the function of a gene. If gene A is homologous to gene B ofwhich the function is known, it is likely to have a similar function. In the structural branch of bioinformatics homology is usedto determine which parts of the protein are important in structure formation and interaction with other proteins. In a techniquecalled homology modelling, this information is used to predict the structure of a protein once the structure of a homologousprotein is known. This currently remains the only way to predict protein structures reliably.
One case example of this is the similar protein homology between hemoglobin in humans and the hemoglobin in legumes(leghemoglobin). Both serve the same purpose of transporting oxygen in both organisms. Though both of these proteins havecompletely different amino acid sequences, their protein structures are virtually identical, which reflects their near identicalpurposes.
Modeling biological systems
Main article: Systems biology
Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism , signal transduction pathways and gene regulatory networks ) to both analyze and visualize thecomplex connections of these cellular processes. Artificial life orvirtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) lifeforms.
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