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Introduction to Bioinformatics: Role of Mathematics and TechnologyBY: Amna Adnan | Category: Bioinformatics | Submitted: 2010-11-11 07:12:43
Article Summary: "Bioinformatics is the combination of Biology, Mathematics and Computer Science. It has its applications in making databases and biological tools to store raw biological data..."
Bioinformatics is one of the disciplines of biology, which considers the use of computers to solve biological problems. By bioinformatics to understand any use of computers to handle biological information. In practice, sometimes it's more narrow definition, under him understand the use of computers for the characterization of molecular components.
The terms bioinformatics and computational biology are often interchangeable, although the latter often indicates the development of specific algorithms and computational methods. It is believed that not all use of computational biology is bioinformatics, egg mathematical modeling - this is not bioinformatics, although it is related to biological problems.
Bioinformatics uses the methods of Applied Mathematics, Statistics and Informatics. Research in computational biology often intersects with systems biology. Major research efforts in this area are aimed at the study of genomes, analysis and prediction of protein structure analysis and prediction of protein interactions with each other and other molecules, as well as modeling of evolution. Bioinformatics and its methods are also used in biochemistry and biophysics. The main line in the projects of bioinformatics - the use of mathematical tools to extract useful information from "noisy" or too voluminous data on the structure of DNA and proteins obtained experimentally.
Analysis of genetic sequences
After 1977 was sequenced phage Phi-X174, the DNA sequence of more and more organisms have been decoded and stored in databases. This data is used to determine the sequences of proteins and regulatory sites. Comparison of the genes within the same or different species may show similar protein functions or relations between species (and thus may be formulated phylogenetic trees). With the growing amount of data has long been impossible to manually analyze the sequence. In our days to search the genomes of thousands of organisms, consisting of billions of base pairs used computer programs. Programs can be uniquely associated with ("align"), similar DNA sequences in the genomes of different species, often these sequences have similar functions, but differences arise because of small mutations, such as the replacement of individual nucleotides, insertion of nucleotides, and their "loss" (deletion). One variant of the alignment used in the sequencing process itself.
The so-called technique of "fractional sequencing" (which was, for example, used by the Institute of Genetic Research to sequence the first bacterial genome, Hemophilic influenza) instead of the full nucleotide sequence gives a sequence of short DNA fragments (each about 600-800 nucleotides in length). The ends of the fragments overlap, and combined properly, give the complete genome. This method quickly gives the results of sequencing, but the assembly of the fragments can be quite challenging for large genomes. The draft of the human genome decoding assembly took several months of computer time. Now this method is used for virtually all genomes, and genome assembly algorithms are one of the most acute problems of bioinformatics at the moment.
Another example of the use of computer analysis of sequences is the automatic search for genes and regulatory sequences in the genome. Not all nucleotides in the genome are used to specify protein sequences. For example, in the genomes of higher organisms, large segments of DNA apparently do not encode proteins and their functional role is not known. Development of algorithms to identify protein-coding regions of the genome is a major challenge of modern bioinformatics.
Bioinformatics helps to bind genomic and proteomic projects, for example, helping in the use of DNA sequences for protein identification.
Computational evolutionary biology
Evolutionary biology examines the origins and emergence of species, as well as their development over time. Computers help evolutionary biologists in several ways:
To study the evolution of a large number of organisms by measuring changes in their DNA, not only in the structure or physiology, compare entire genomes (see BLAST), which allows to study more complex evolutionary events, such as gene duplication, lateral gene transfer and to predict bacterial factors specialist 'build computer models of populations in order to predict the behavior of the system in time track the emergence of publications that contain information about a large number of species.
Area in computer science that uses genetic algorithms is sometimes confused with computer evolutionary biology. Work in this area uses specialized software to improve the algorithms and calculations, and is based on evolutionary principles, such as replication, diversification through recombination or mutation and survival in natural selection.
Biological diversity of ecosystems can be defined as a complete genetic set of a particular environment, consisting of all living species, would be a biofilm in an abandoned mine, a drop of sea water, a handful of soil or the entire biosphere of planet Earth. To collect the species names, descriptions, habitat distribution, genetic information is used databases. Specialized software is used to find, visualize and analyze information, and, more importantly, provide it to other people. Computer simulations model such things as population dynamics, or calculate the overall genetic health of the culture in agronomy. One of the most important potentials of this field is the analysis of DNA sequences or complete genomes of entire endangered species, will remember the results of a genetic experiment of nature in the computer and can be used again in the future, even if these species will die out completely.
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