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In biology, Bioinformatics i /ˌbaɪ.oʊˌɪnfərˈmætɪks/ is an interdisciplinary field that develops and improves on methods for storing, retrieving, organizing and analyzing biological data. A major activity in bioinformatics is to develop software tools to generate useful biological knowledge. Bioinformatics has become an important part of many areas of biology. In experimental molecular biology, bioinformatics techniques such as image and signal processing allow extraction of useful results from large amounts of raw data. In the field of genetics and genomics, it aids in sequencing and annotating genomes and their observed mutations. It plays a role in the textual mining of biological literature and the development of biological and gene ontologies to organize and query biological data. It plays a role in the analysis of gene and protein expression and regulation. Bioinformatics tools aid in the comparison of genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of systems biology. In structural biology, it aids in the simulation and modeling of DNA, RNA, and protein structures as well as molecular interactions.

Map of the human X chromosome (from the NCBI website). Assembly of the human genome is one of the greatest achievements of bioinformatics.

Bioinformatics uses many areas of computer science, mathematics and engineering to process biological data. Complex machines are used to read in biological data at a much faster rate than before. Databases and information systems are used to store and organize biological data. Analyzing biological data may involve algorithms in artificial intelligence, soft computing, data mining, image processing, and simulation. The algorithms in turn depend on theoretical foundations such as discrete mathematics, control theory, system theory, information theory, and statistics. Commonly used software tools and technologies in the field include Java, C#, XML, Perl, C, C++, Python, R, SQL, CUDA, MATLAB, and spreadsheet applications.[1][2][3]

1 Introduction 1.1 History 1.2 Goals 1.3 Approaches 2 Major research areas 2.1 Sequence analysis 2.2 Genome annotation 2.3 Computational evolutionary biology 2.4 Literature analysis 2.5 Analysis of gene expression

10 Network and systems biology 2.2.[7] Another significant pioneer in the field was Margaret Oakley Dayhoff.11 High-throughput image analysis 2. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could access existing data as well as submit new or revised data. the term bioinformatics was re-discovered to refer to the creation and maintenance of a database to store biological information such as nucleotide sequences and amino acid sequences."[8] At the beginning of the "genomic revolution". who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. in 1970 Paulien Hogeweg. director of the National Center for Biotechnology Information.7 Analysis of protein expression 2.[4][5][6] This definition placed bioinformatics as a field parallel to biophysics or biochemistry (biochemistry is the study of chemical processes in biological systems).2.1 Open-source bioinformatics software 3. as the "mother and father of bioinformatics.2 Molecular Interaction 2.2 Web services in bioinformatics 3.6 Analysis of regulation 2.8 Analysis of mutations in cancer 2.12 Structural bioinformatic approaches 2.[4] Examples of relevant biological information processes studied in the early days of bioinformatics are the formation of complex social interaction structures by simple behavioral rules. accumulation and processing in biological systems.1 Prediction of protein structure 2. One early contributor to bioinformatics was Elvin A. who has been hailed by David Lipman.1 Docking algorithms 3 Software and tools 3.3 Bioinformatics workflow management systems 3. coined the term "Bioinformatics" to refer to the study of information processes in biotic systems. and the information accumulation and maintenance in models of prebiotic evolution. Goals .9 Comparative genomics 2.4 Rosalind 4 Conferences 5 See also 6 References 7 Further reading 8 External links Introduction History Building on the recognition of the importance of information transmission.12.12.12. Kabat.

Static Sequences – Proteins.[9] The actual process of analyzing and interpreting data is referred to as computational biology.In order to study how normal cellular activities are altered in different disease states. Therefore. and theory to solve formal and practical problems arising from the management and analysis of biological data. use and management of. Bioinformatics now entails the creation and advancement of databases. drug discovery. protein domains. algorithms. protein structure alignment. and creating and viewing 3-D models of protein structures. Over the past few decades rapid developments in genomic and other molecular research technologies and developments in information technologies have combined to produce a tremendous amount of information related to molecular biology. and protein structures.g. Nucleic acids and Peptides Interaction data among the above entities including microarray data and Networks of proteins. transcription and . Ligands (including metabolites and drugs) and Peptides (structures studied with bioinformatics tools are not considered static anymore and their dynamics is often the core of the structural studies) Systems Biology comes under this category including reaction fluxes and variable concentrations of metabolites Multi-Agent Based modelling approaches capturing cellular events such as signalling. For example. aligning different DNA and protein sequences to compare them. metabolites Dynamic Structures – Proteins. and cluster protein sequences into families of related sequences. Major research efforts in the field include sequence alignment. Examples include: pattern recognition. machine learning algorithms. prediction of gene expression and protein– protein interactions. Bioinformatics is the name given to these mathematical and computing approaches used to glean understanding of biological processes. genome-wide association studies. protein structure prediction. The primary goal of bioinformatics is to increase the understanding of biological processes. various types of information. drug design. the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. gene finding. This includes nucleotide and amino acid sequences. There are two fundamental ways of modelling a Biological system (e. predict protein structure and/or function. is its focus on developing and applying computationally intensive techniques to achieve this goal. data mining. the biological data must be combined to form a comprehensive picture of these activities.. living cell) both coming under Bioinformatic approaches. computational and statistical techniques. Important sub-disciplines within bioinformatics and computational biology include: the development and implementation of tools that enable efficient access to. Approaches Common activities in bioinformatics include mapping and analyzing DNA and protein sequences. What sets it apart from other approaches. Nucleic acids. and the modeling of evolution. methods to locate a gene within a sequence. genome assembly. and visualization. the development of new algorithms (mathematical formulas) and statistics with which to assess relationships among members of large data sets. however.

Bioinformatics helps to bridge the gap between genome and proteome projects — for example. The first genome annotation software system was designed in 1995 by Owen White. This sequence information is analyzed to determine genes that encode polypeptides (proteins). Shotgun sequencing is the method of choice for virtually all genomes sequenced today. for example. multiprocessor computers to assemble the fragments.[11] These programs can compensate for mutations (exchanged. or relations between species (the use of molecular systematics to construct phylogenetic trees). containing over 190 billion nucleotides. The ends of these fragments overlap and.[10] the DNA sequences of thousands of organisms have been decoded and stored in databases. Another aspect of bioinformatics in sequence analysis is annotation. See also: sequence analysis. it may take many days of CPU time on large-memory. and sequence motif Genome annotation Main article: Gene finding In the context of genomics. however. For a genome as large as the human genome. structural motifs. White built a software system to find the genes . and the resulting assembly will usually contain numerous gaps that have to be filled in later. large parts of the DNA do not serve any obvious purpose. RNA genes. can be used to reconstruct the complete genome. A variant of this sequence alignment is used in the sequencing process itself. and repetitive sequences. annotation is the process of marking the genes and other biological features in a DNA sequence. by The Institute for Genomic Research to sequence the first bacterial genome. Within the genomes of higher organisms. Instead it generates the sequences of many thousands of small DNA fragments (ranging from 35 to 900 nucleotides long. Today. This involves computational gene finding to search for protein-coding genes. computer programs such as BLAST are used daily to search sequences from more than 260 000 organisms. the bacterium Haemophilus influenzae.reaction dynamics A broad sub-category under bioinformatics is structural bioinformatics. This so-called junk DNA may. and genome assembly algorithms are a critical area of bioinformatics research. and other functional sequences within a genome. RNA genes. contain unrecognized functional elements. in the use of DNA sequences for protein identification. regulatory sequences. depending on the sequencing technology). Haemophilus influenzae)[12] does not produce entire chromosomes. With the growing amount of data. sequence mining. Not all of the nucleotides within a genome are part of genes. but the task of assembling the fragments can be quite complicated for larger genomes. Shotgun sequencing yields sequence data quickly. but not identical. The so-called shotgun sequencing technique (which was used. who was part of the team at The Institute for Genomic Research that sequenced and analyzed the first genome of a free-living organism to be decoded. to identify sequences that are related. it long ago became impractical to analyze DNA sequences manually. deleted or inserted bases) in the DNA sequence. when aligned properly by a genome assembly program. A comparison of genes within a species or between different species can show similarities between protein functions. Major research areas Sequence analysis Main articles: Sequence alignment and Sequence database Since the Phage Φ-X174 was sequenced in 1977. sequence profiling tool.

and a major research area in computational biology involves developing statistical tools to separate signal from noise in high-throughput gene expression studies. and to make initial assignments of function to those genes. The area of research within computer science that uses genetic algorithms is sometimes confused with computational evolutionary biology. Literature analysis Main article: Text mining The growth in the number of published literature makes it virtually impossible to read every paper. such as the GeneMark program trained and used to find protein-coding genes in Haemophilus influenzae. rather than through physical taxonomy or physiological observations alone. serial analysis of gene expression (SAGE) tag sequencing. Analysis of gene expression The expression of many genes can be determined by measuring mRNA levels with multiple techniques including microarrays. which permits the study of more complex evolutionary events. resulting in disjointed sub-fields of research. also known as "Whole Transcriptome Shotgun Sequencing" (WTSS). build complex computational models of populations to predict the outcome of the system over time [13] track and share information on an increasingly large number of species and organisms Future work endeavours to reconstruct the now more complex tree of life. Most current genome annotation systems work similarly. but the programs available for analysis of genomic DNA. compare entire genomes. but the two areas are not necessarily related. RNA-Seq. massively parallel signature sequencing (MPSS). Computational evolutionary biology Evolutionary biology is the study of the origin and descent of species. the transfer RNAs. or various applications of multiplexed in-situ hybridization. such as gene duplication. horizontal gene transfer. expressed cDNA sequence tag (EST) sequencing. more recently. For example: abbreviation recognition – identify the long-form and abbreviation of biological terms. it has enabled researchers to: trace the evolution of a large number of organisms by measuring changes in their DNA. and the prediction of factors important in bacterial speciation.(fragments of genomic sequence that encode proteins). Such studies are often used to determine the genes implicated in a disorder: one might compare microarray data from cancerous epithelial cells to data from non-cancerous cells to determine the transcripts that are up-regulated and down-regulated in a particular population of cancer cells. Literature analysis aims to employ computational and statistical linguistics to mine this growing library of text resources. are constantly changing and improving. Informatics has assisted evolutionary biologists in several key ways. named entity recognition – recognizing biological terms such as gene names protein-protein interaction – identify which proteins interact with which proteins from text The area of research draws from statistics and computational linguistics. as well as their change over time. All of these techniques are extremely noise-prone and/or subject to bias in the biological measurement. .

The data is often found to contain considerable variability. starvation. Another type of data that requires novel informatics development is the analysis of lesions found to be recurrent among many tumors. promoter analysis involves the identification and study of sequence motifs in the DNA surrounding the coding region of a gene. Bioinformaticians continue to produce specialized automated systems to manage the sheer volume of sequence data produced. For example. has been actually proposed to address various issues specific to gene discovery problems such as consistent co-expression of genes over multiple microarray datasets. one might compare stages of the cell cycle. the genomes of affected cells are rearranged in complex or even unpredictable ways. Analysis of mutations in cancer In cancer. the latter involves the problem of matching large amounts of mass data against predicted masses from protein sequence databases. Expression data can be used to infer gene regulation: one might compare microarray data from a wide variety of states of an organism to form hypotheses about the genes involved in each state. hierarchical clustering. Comparative genomics Main article: Comparative genomics The core of comparative genome analysis is the establishment of the correspondence between genes (orthology . and single-nucleotide polymorphism arrays to detect known point mutations.Analysis of regulation Regulation is the complex orchestration of events starting with an extracellular signal such as a hormone and leading to an increase or decrease in the activity of one or more proteins. Examples of clustering algorithms applied in gene clustering are k-means clustering. but incomplete peptides from each protein are detected. One can then apply clustering algorithms to that expression data to determine which genes are co-expressed. and thus Hidden Markov model and change-point analysis methods are being developed to infer real copy number changes. and they create new algorithms and software to compare the sequencing results to the growing collection of human genome sequences and germline polymorphisms. the upstream regions (promoters) of co-expressed genes can be searched for over-represented regulatory elements. and the complicated statistical analysis of samples where multiple.[14][15] Analysis of protein expression Protein microarrays and high throughput (HT) mass spectrometry (MS) can provide a snapshot of the proteins present in a biological sample. These motifs influence the extent to which that region is transcribed into mRNA.). along with various stress conditions (heat shock. and consensus clustering methods such as the BiCoPaM. self-organizing maps (SOMs). New physical detection technologies are employed. the former approach faces similar problems as with microarrays targeted at mRNA. such as oligonucleotide microarrays to identify chromosomal gains and losses (called comparative genomic hybridization). These detection methods simultaneously measure several hundred thousand sites throughout the genome. generate terabytes of data per experiment. The later. namely Bi-CoPaM. and when used in highthroughput to measure thousands of samples. Bioinformatics techniques have been applied to explore various steps in this process. Again the massive amounts and new types of data generate new opportunities for bioinformaticians. etc. Massive sequencing efforts are used to identify previously unknown point mutations in a variety of genes in cancer. In a single-cell organism. or noise. Bioinformatics is very much involved in making sense of protein microarray and HT MS data. For example.

Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms. small molecules. large chromosomal segments undergo duplication. and others. Although these systems are not unique to biomedical imagery. deletion and insertion. fixed parameter and approximation algorithms for problems based on parsimony models to Markov Chain Monte Carlo algorithms for Bayesian analysis of problems based on probabilistic models. Bioimage informatics) morphometrics clinical image analysis and visualization determining the real-time air-flow patterns in breathing lungs of living animals quantifying occlusion size in real-time imagery from the development of and recovery during arterial injury making behavioral observations from extended video recordings of laboratory animals infrared measurements for metabolic activity determination inferring clone overlaps in DNA mapping. A fully developed analysis system may completely replace the observer. High-throughput image analysis Computational technologies are used to accelerate or fully automate the processing. Ultimately. transposition. inversion. often leading to rapid speciation. It is these intergenomic maps that make it possible to trace the evolutionary processes responsible for the divergence of two genomes. such as proteins. gene expression data. the Sulston score Structural bioinformatic approaches . whole genomes are involved in processes of hybridization. network biology often attempts to integrate many different data types. polyploidization and endosymbiosis. ranging from exact. Modern image analysis systems augment an observer's ability to make measurements from a large or complex set of images. signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes. Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism. cytohistopathology. who have recourse to a spectra of algorithmic. Although biological networks can be constructed from a single type of molecule or entity (such as genes). and Interactome Network analysis seeks to understand the relationships within biological networks such as metabolic or proteinprotein interaction networks. Many of these studies are based on the homology detection and protein families computation. objectivity. e. The complexity of genome evolution poses many exciting challenges to developers of mathematical models and algorithms. point mutations affect individual nucleotides. heuristics. A multitude of evolutionary events acting at various organizational levels shape genome evolution. which are all connected physically and/or functionally. Biological network. quantification and analysis of large amounts of high-information-content biomedical imagery. Network and systems biology Main articles: Computational systems biology. or speed.g.The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis) or other genomic features in different organisms. Some examples are: high-throughput and high-fidelity quantification and sub-cellular localization (high-content screening. biomedical imaging is becoming more important for both diagnostics and research. by improving accuracy. statistical and mathematical techniques. At a higher level. lateral transfer. At the lowest level.

The amino acid sequence of a protein. this information is used to predict the structure of a protein once the structure of a homologous protein is known. their protein structures are virtually identical. See also: structural motif and structural domain.a. One central question for the . In the vast majority of cases. termed docking algorithms for studying molecular interactions. homology is used to predict the function of a gene: if the sequence of gene A. such as the bovine spongiform encephalopathy – a.) Knowledge of this structure is vital in understanding the function of the protein. Most efforts have so far been directed towards heuristics that work most of the time. For lack of better terms. can be easily determined from the sequence on the gene that codes for it. A viable general solution to such predictions remains an open problem. ligands and peptides.k. Types of interactions most often encountered in the field include – Protein–ligand (including drug). Other techniques for predicting protein structure include protein threading and de novo (from scratch) physicsbased modeling. Mad Cow Disease – prion. See also: protein–protein interaction prediction. This currently remains the only way to predict protein structures reliably. this primary structure uniquely determines a structure in its native environment. tens of thousands of protein three-dimensional structures have been determined by X-ray crystallography and Protein nuclear magnetic resonance spectroscopy (protein NMR). protein–protein and protein–peptide. Molecular Interaction Efficient software is available today for studying interactions among proteins. In a technique called homology modeling. is homologous to the sequence of gene B. In the structural branch of bioinformatics. One of the key ideas in bioinformatics is the notion of homology. One example of this is the similar protein homology between hemoglobin in humans and the hemoglobin in legumes (leghemoglobin). the so-called primary structure. whose function is known. there are exceptions. (Of course. which reflects their near identical purposes. Molecular dynamic simulation of movement of atoms about rotatable bonds is the fundamental principle behind computational algorithms. whose function is unknown. Docking algorithms Main article: Protein–protein docking In the last two decades. Both serve the same purpose of transporting oxygen in the organism. In the genomic branch of bioinformatics. structural information is usually classified as one of secondary.Prediction of protein structure Main article: Protein structure prediction Protein structure prediction is another important application of bioinformatics. tertiary and quaternary structure. Though both of these proteins have completely different amino acid sequences. homology is used to determine which parts of a protein are important in structure formation and interaction with other proteins. one could infer that B may share A's function.

to integrative. They may also provide de facto standards and shared object models for assisting with the challenge of bioinformation integration. or a workflow.[citation needed] The availability of these service-oriented bioinformatics resources demonstrate the applicability of web-based bioinformatics solutions.[16] The combination of a continued need for new algorithms for the analysis of emerging types of biological readouts. in a Bioinformatics application. BioJava. EMBOSS. Software and tools Software tools for bioinformatics range from simple command-line tools. or community-supported plug-ins in commercial applications. standalone or webbased interface. . to more complex graphical programs and standalone web-services available from various bioinformatics companies or public institutions.NET Bio. BioRuby. The main advantages derive from the fact that end users do not have to deal with software and database maintenance overheads. Bioclipse. The open source tools often act as incubators of ideas. Basic bioinformatics services are classified by the EBI into three categories: SSS (Sequence Search Services). though it seems that there is still much work to be done in this field. and freely available open code bases have helped to create opportunities for all research groups to contribute to both bioinformatics and the range of open-source software available. without doing protein–protein interaction experiments.[17] Web services in bioinformatics SOAP. Taverna workbench. Open-source bioinformatics software Many free and open-source software tools have existed and continued to grow since the 1980s. Biopython. A variety of methods have been developed to tackle the Protein–protein docking problem. and range from a collection of standalone tools with a common data format under a single. the potential for innovative in silico experiments.and REST-based interfaces have been developed for a wide variety of bioinformatics applications allowing an application running on one computer in one part of the world to use algorithms. Such systems are designed to provide an easy-to-use environment for individual application scientists themselves to create their own workflows . and UGENE. data and computing resources on servers in other parts of the world. and BSA (Biological Sequence Analysis). the non-profit Open Bioinformatics Foundation[16] have supported the annual Bioinformatics Open Source Conference (BOSC) since 2000. distributed and extensible bioinformatics workflow management systems.biological scientist is whether it is practical to predict possible protein–protein interactions only based on these 3D shapes. Bioinformatics workflow management systems Main article: Bioinformatics workflow management systems A Bioinformatics workflow management system is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps. The range of open-source software packages includes titles such as Bioconductor. MSA (Multiple Sequence Alignment). BioPerl. regardless of their funding arrangements. In order to maintain this tradition and create further opportunities.

[23] Conferences There are several large conferences that are concerned with bioinformatics. European Conference on Computational Biology (ECCB). it hosts over 8.[18][19][20][21][22] Rosalind users learn bioinformatics concepts through a problem tree that builds up biological. there are at least four platforms giving this service: Galaxy.provide interactive tools for the scientists enabling them to execute their workflows and view their results in real-time simplify the process of sharing and reusing workflows between the It was recognized by Homolog. See also Computational biology Computational genomics Health informatics Computational biomodeling Functional genomics Phylogenetics Bioinformatics companies Margaret Oakley Dayhoff International Society for Computational Biology List of scientific journals in bioinformatics List of open-source bioinformatics software Jumping library References . algorithmic. Rosalind Rosalind is an educational resource and web project for learning bioinformatics through problem solving and computer programming. The project's name commemorates Rosalind as the Best Educational Resource of 2012 in their review of the Top Bioinformatics Contributions of 2012 (http://www. allowing for the project to also be used for automated homework testing in existing classes. Rosalind will be used to teach the first Bioinformatics Algorithms course on Coursera in 2013. Watson and Francis Crick.000 problem solvers. As of June 2013. Taverna and Anduril. Rosalind is a joint project between the University of California at San Diego and Saint Petersburg Academic University along with the Russian Academy of Sciences. and programming knowledge concurrently. Each problem is checked automatically. enable scientists to track the provenance of the workflow execution results and the workflow creation steps. Some of the most notable examples are Intelligent Systems for Molecular Biology (ISMB). whose X-ray crystallography with Raymond Gosling facilitated the discovery of the DNA double helix by James D. Research in Computational Molecular Biology (RECOMB) and American Society of Mass Spectrometry (ASMS). Kepler. Currently.homolog.

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