Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Applied mathematics is a branch of Mathematics that concerns itself with the mathematical techniques typically used in the application of mathematical knowledge to other domains Informatics is the science of Information, the practice of Information processing, and the engineering of Information systems. Statistics is a mathematical science pertaining to the collection analysis interpretation or explanation and presentation of Data. Computer science (or computing science) is the study and the Science of the theoretical foundations of Information and Computation and their Chemistry (from Egyptian kēme (chem meaning "earth") is the Science concerned with the composition structure and properties Biochemistry is the study of the chemical processes in living Organisms It deals with the Structure and function of cellular components such as Foundations of modern biology There are five unifying principles In Chemistry, a molecule is defined as a sufficiently stable electrically neutral group of at least two Atoms in a definite arrangement held together by The core principle of these techniques is using computing resources in order to solve problems on scales of magnitude far too great for human discernment. Research in computational biology often overlaps with systems biology. Systems biology is a biology-based inter-disciplinary study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution. In Bioinformatics, a sequence alignment is a way of arranging the Primary sequences of DNA, RNA, or Protein to identify regions of Gene finding typically refers to the area of Computational biology that is concerned with algorithmically identifying stretches of sequence usually genomic DNA Genome projects are Scientific endeavours that ultimately aim to determine the complete Genome sequence of an Organism (be it an Animal, a Structural alignment is a form of Sequence alignment based on comparison of shape Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry. Gene expression is the process by which inheritable information from a Gene, such as the DNA sequence, is made into a functional Gene product, such Protein-protein interactions refer to the association of Protein molecules and the study of these associations from the perspective of Biochemistry, Signal transduction eVolution is the third Album by eLDee, it was due to be released in 2008

Contents 1 Introduction 2 Major research areas 2.1 Sequence analysis 2.2 Genome annotation 2.3 Computational evolutionary biology 2.4 Measuring biodiversity 2.5 Analysis of gene expression 2.6 Analysis of regulation 2.7 Analysis of protein expression 2.8 Analysis of mutations in cancer 2.9 Prediction of protein structure 2.10 Comparative genomics 2.11 Modeling biological systems 2.12 High-throughput image analysis 2.13 Protein-protein docking 3 Software tools 4 See also 4.1 Related topics 4.2 Related fields 5 References 6 External links

Introduction

The terms bioinformatics and computational biology are often used interchangeably. However bioinformatics more properly refers to the creation and advancement of algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. Computational biology, on the other hand, refers to hypothesis-driven investigation of a specific biological problem using computers, carried out with experimental or simulated data, with the primary goal of discovery and the advancement of biological knowledge. Put more simply, bioinformatics is concerned with the information while computational biology is concerned with the hypotheses. A similar distinction is made by National Institutes of Health in their working definitions of Bioinformatics and Computational Biology, where it is further emphasized that there is a tight coupling of developments and knowledge between the more hypothesis-driven research in computational biology and technique-driven research in bioinformatics. "NIH" redirects here For other meanings of NIH see NIH (disambiguation. Bioinformatics is also often specified as an applied subfield of the more general discipline of Biomedical informatics. Biomedical informatics is the broad discipline concerned with the study and application of Computer science, Information science, Informatics, Cognitive

A common thread in projects in bioinformatics and computational biology is the use of mathematical tools to extract useful information from data produced by high-throughput biological techniques such as genome sequencing. The term DNA sequencing encompasses biochemical methods for determining the order of the Nucleotide bases Adenine, Guanine, Cytosine A representative problem in bioinformatics is the assembly of high-quality genome sequences from fragmentary "shotgun" DNA sequencing. For the sense of "sequencing" used in Electronic music, see the Music sequencer article Other common problems include the study of gene regulation to perform expression profiling using data from microarrays or mass spectrometry. Gene modulation redirects here For information on therapeutic regulation of gene expression see Therapeutic gene modulation. For terminology see glossary below A DNA microarray is a High-throughput technology used in Molecular biology and in Mass spectrometry is an analytical technique that identifies the chemical composition of a compound or sample based on the Mass-to-charge ratio of charged particles

Major research areas

Sequence analysis

Main articles: Sequence alignment and Sequence database

Since the Phage Φ-X174 was sequenced in 1977, the DNA sequences of hundreds of organisms have been decoded and stored in databases. In Bioinformatics, a sequence alignment is a way of arranging the Primary sequences of DNA, RNA, or Protein to identify regions of In the field of Bioinformatics, a sequence database is a large collection of DNA, Protein, or other sequences stored on a computer The phi X 174 (or phi X) Bacteriophage was the first DNA-based Genome to be sequenced by Fred Sanger and his team in 1977. For the sense of "sequencing" used in Electronic music, see the Music sequencer article A DNA sequence or genetic sequence is a succession of letters representing the Primary structure of a real or hypothetical DNA Molecule The information is analyzed to determine genes that encode polypeptides, as well as regulatory sequences. Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino A comparison of genes within a species or between different species can show similarities between protein functions, or relations between species (the use of molecular systematics to construct phylogenetic trees). In Biology, a species is one of the basic units of Biological classification and a Taxonomic rank. A phylogenetic tree, also called an evolutionary tree, is a tree showing the Evolutionary relationships among various biological Species or other With the growing amount of data, it long ago became impractical to analyze DNA sequences manually. Today, computer programs are used to search the genome of thousands of organisms, containing billions of nucleotides. Computer programs (also software programs, or just programs) are instructions for a Computer. In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group These programs would compensate for mutations (exchanged, deleted or inserted bases) in the DNA sequence, in order to identify sequences that are related, but not identical. A variant of this sequence alignment is used in the sequencing process itself. In Bioinformatics, a sequence alignment is a way of arranging the Primary sequences of DNA, RNA, or Protein to identify regions of The so-called shotgun sequencing technique (which was used, for example, by The Institute for Genomic Research to sequence the first bacterial genome, Haemophilus influenzae) does not give a sequential list of nucleotides, but instead the sequences of thousands of small DNA fragments (each about 600-800 nucleotides long). In Genetics, shotgun sequencing, also known as shotgun cloning, is a method used for Sequencing long DNA strands The Institute for Genomic Research ( TIGR) was a Non-profit Genomics research institute founded in 1992 by Craig Venter in The ends of these fragments overlap and, when aligned in the right way, make up the complete genome. Shotgun sequencing yields sequence data quickly, but the task of assembling the fragments can be quite complicated for larger genomes. In the case of the Human Genome Project, it took several months of CPU time (on a circa-2000 vintage DEC Alpha computer) to assemble the fragments. The Human Genome Project (HGP was an international Scientific research project with a primary goal to determine the sequence of chemical base pairs which make up DNA Alpha, originally known as Alpha AXP, was a 64-bit Reduced instruction set computer (RISC Instruction set architecture (ISA developed Shotgun sequencing is the method of choice for virtually all genomes sequenced today, and genome assembly algorithms are a critical area of bioinformatics research.

Another aspect of bioinformatics in sequence analysis is the automatic search for genes and regulatory sequences within a genome. Gene finding typically refers to the area of Computational biology that is concerned with algorithmically identifying stretches of sequence usually genomic DNA Not all of the nucleotides within a genome are genes. 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. In Molecular biology, junk DNA is a provisional label for the portions of the DNA sequence of a Chromosome or a Genome for which no Bioinformatics helps to bridge the gap between genome and proteome projects--for example, in the use of DNA sequences for protein identification. The proteome is the entire complement of Proteins expressed by a genome cell tissue or organism

See also: sequence analysis, sequence profiling tool, sequence motif. The term "sequence analysis" in biology implies subjecting a DNA or Peptide sequence to Sequence alignment, Sequence databases A sequence profiling tool in Bioinformatics is a type of Software that presents information related to a genetic sequence gene name or keyword input In Genetics, a sequence motif is a Nucleotide or amino-acid Sequence pattern that is widespread and has or is conjectured to have a biological

Genome annotation

Main article: Gene finding

In the context of genomics, annotation is the process of marking the genes and other biological features in a DNA sequence. Gene finding typically refers to the area of Computational biology that is concerned with algorithmically identifying stretches of sequence usually genomic DNA The first genome annotation software system was designed in 1995 by Dr. Owen White, who was part of the team that sequenced and analyzed the first genome of a free-living organism to be decoded, the bacterium Haemophilus influenzae. Haemophilus influenzae, formerly called Pfeiffer's bacillus or Bacillus influenzae, is a non-motile Gram-negative Coccobacillus Dr. White built a software system to find the genes (places in the DNA sequence that encode a protein), the transfer RNA, and other features, and to make initial assignments of function to those genes. Most current genome annotation systems work similarly, but the programs available for analysis of genomic DNA are constantly changing and improving.

Computational evolutionary biology

Evolutionary biology is the study of the origin and descent of species, as well as their change over time. Evolutionary biology is a sub-field of Biology concerned with the origin of Species from a Common descent, and Descent of species In Biology, a species is one of the basic units of Biological classification and a Taxonomic rank. Informatics has assisted evolutionary biologists in several key ways; it has enabled researchers to:

• trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone,
• more recently, compare entire genomes, which permits the study of more complex evolutionary events, such as gene duplication, lateral gene transfer, and the prediction of factors important in bacterial speciation,
• build complex computational models of populations to predict the outcome of the system over time
• 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. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby Gene duplication (or chromosomal duplication) is any duplication of a region of DNA that contains a Gene; it may occur as an error in Homologous Speciation is the Evolutionary process by which new biological Species arise A phylogenetic tree, also called an evolutionary tree, is a tree showing the Evolutionary relationships among various biological Species or other

The area of research within computer science that uses genetic algorithms is sometimes confused with computational evolutionary biology, but the two areas are unrelated. Computer science (or computing science) is the study and the Science of the theoretical foundations of Information and Computation and their A genetic algorithm (GA is a Search technique used in Computing to find exact or Approximate solutions to optimization and Search

Measuring biodiversity

Biodiversity of an ecosystem might be defined as the total genomic complement of a particular environment, from all of the species present, whether it is a biofilm in an abandoned mine, a drop of sea water, a scoop of soil, or the entire biosphere of the planet Earth. Biodiversity is the variation of Life forms within a given Ecosystem, Biome or for the entire Earth. The biosphere is the broadest level of ecological study the global sum of all Ecosystems. EARTH was a short-lived Japanese vocal trio which released 6 singles and 1 album between 2000 and 2001 Databases are used to collect the species names, descriptions, distributions, genetic information, status and size of populations, habitat needs, and how each organism interacts with other species. In Biology, a species is one of the basic units of Biological classification and a Taxonomic rank. In Biology a population is the collection of inter-breeding organisms of a particular Species; in Sociology A habitat (which is Latin for "it inhabits" is an Ecological or environmental area that is inhabited by a particular Species. Specialized software programs are used to find, visualize, and analyze the information, and most importantly, communicate it to other people. Computer simulations model such things as population dynamics, or calculate the cumulative genetic health of a breeding pool (in agriculture) or endangered population (in conservation). Agriculture refers to the production of goods through the growing of plants and fungi and the raising of domesticated Animals The study of agriculture "Conservation Biology" redirects here For the Scientific journal, see Conservation Biology (journal. One very exciting potential of this field is that entire DNA sequences, or genomes of endangered species can be preserved, allowing the results of Nature's genetic experiment to be remembered in silico, and possibly reused in the future, even if that species is eventually lost. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby An endangered species is a population of an organism which is at risk of becoming Extinct because it is either few in numbers or threatened by changing environmental or predation In Silico is the second full-length studio album by Australian Drum and bass band Pendulum, released in Australia and

Important projects: Species 2000 project; uBio Project.

Analysis of gene expression

The expression of many genes can be determined by measuring mRNA levels with multiple techniques including microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression (SAGE) tag sequencing, massively parallel signature sequencing (MPSS), or various applications of multiplexed in-situ hybridization. Gene expression is the process by which inheritable information from a Gene, such as the DNA sequence, is made into a functional Gene product, such Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product For terminology see glossary below A DNA microarray is a High-throughput technology used in Molecular biology and in An expressed sequence tag or EST is a short sub-sequence of a transcribed spliced nucleotide sequence (either Protein -coding or not Serial analysis of gene expression (SAGE is a technique used by molecular biologists to produce a snapshot of the Messenger RNA population in a sample of interest All of these techniques are extremely noise-prone and/or subject to bias in the biological measurement, and a major research area in computational biology involves developing statistical tools to separate signal from noise in high-throughput gene expression studies. In the fields of communications, Signal processing, and in Electrical engineering more generally a signal is any time-varying or spatial-varying quantity is a one volume manga created by Tsutomu Nihei as a prequel to his ten-volume work Blame!. 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. In biology and medicine epithelium is a tissue composed of cells that line the cavities and surfaces of structures throughout the body

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. Hormones (from Greek ὁρμή - "impetus" are chemicals released by cells that affect cells in other parts of the body Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Bioinformatics techniques have been applied to explore various steps in this process. For example, promoter analysis involves the identification and study of sequence motifs in the DNA surrounding the coding region of a gene. In Genetics, a sequence motif is a Nucleotide or amino-acid Sequence pattern that is widespread and has or is conjectured to have a biological These motifs influence the extent to which that region is transcribed into mRNA. 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. In a single-cell organism, one might compare stages of the cell cycle, along with various stress conditions (heat shock, starvation, etc. The cell cycle, or cell-division cycle, is the series of events that take place in a eukaryotic cell leading to its replication ). One can then apply clustering algorithms to that expression data to determine which genes are co-expressed. Clustering is the classification of objects into different groups or more precisely the partitioning of a Data set into Subsets (clusters For example, the upstream regions (promoters) of co-expressed genes can be searched for over-represented regulatory elements. A regulatory sequence (also called a regulatory region or a regulatory area) is a segment of DNA where regulatory proteins such as Transcription

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. Mass spectrometry is an analytical technique that identifies the chemical composition of a compound or sample based on the Mass-to-charge ratio of charged particles Bioinformatics is very much involved in making sense of protein microarray and HT MS data; the former approach faces similar problems as with microarrays targeted at mRNA, the latter involves the problem of matching large amounts of mass data against predicted masses from protein sequence databases, and the complicated statistical analysis of samples where multiple, but incomplete peptides from each protein are detected.

Analysis of mutations in cancer

In cancer, the genomes of affected cells are rearranged in complex or even unpredictable ways. Massive sequencing efforts are used to identify previously unknown point mutations in a variety of genes in cancer. A point mutation, or single base substitution, is a type of Mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance Cancer (medical term Malignant Neoplasm) is a class of Diseases in which a group of cells display uncontrolled Bioinformaticians continue to produce specialized automated systems to manage the sheer volume of sequence data produced, and they create new algorithms and software to compare the sequencing results to the growing collection of human genome sequences and germline polymorphisms. The human genome is the Genome of Homo sapiens, which is stored on 23 chromosome pairs In Biology and Genetics, the germline of a mature or developing individual is the line (sequence of Germ cells that have genetic material that New physical detection technology are employed, such as oligonucleotide microarrays to identify chromosomal gains and losses (called comparative genomic hybridization), and single nucleotide polymorphism arrays to detect known point mutations. An oligonucleotide (or oligo) is a short segment of RNA or DNA, typically with twenty or fewer bases. Comparative genomic hybridization ( CGH) or Chromosomal Microarray Analysis ( CMA) is a molecular- Cytogenetic method for the analysis of A single nucleotide polymorphism ( SNP, pronounced snip) is a DNA sequence variation occurring when a single Nucleotide - A, T These detection methods simultaneously measure several hundred thousand sites throughout the genome, and when used in high-throughput to measure thousands of samples, generate terabytes of data per experiment. A terabyte (derived from the prefix Tera- and commonly abbreviated TB) is a measurement term for data storage capacity. Again the massive amounts and new types of data generate new opportunities for bioinformaticians. The data is often found to contain considerable variability, or noise, and thus Hidden Markov model and change-point analysis methods are being developed to infer real copy number changes. is a one volume manga created by Tsutomu Nihei as a prequel to his ten-volume work Blame!. A hidden Markov model ( HMM) is a Statistical model in which the system being modeled is assumed to be a Markov process with unknown parameters and the

Another type of data that requires novel informatics development is the analysis of lesions found to be recurrent among many tumors .

Prediction of protein structure

Main article: Protein structure prediction

Protein structure prediction is another important application of bioinformatics. Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry. The amino acid sequence of a protein, the so-called primary structure, can be easily determined from the sequence on the gene that codes for it. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including In the vast majority of cases, this primary structure uniquely determines a structure in its native environment. (Of course, there are exceptions, such as the bovine spongiform encephalopathy - aka Mad Cow Disease - prion. Bovine Spongiform Encephalopathy ( BSE) commonly known as Mad-Cow Disease ( MCD) is a fatal Neurodegenerative disease in Cattle Bovine Spongiform Encephalopathy ( BSE) commonly known as Mad-Cow Disease ( MCD) is a fatal Neurodegenerative disease in Cattle A prion (ˈpriːɒn is thought to be an infectious agent that according to current scientific consensus is comprised entirely of a propagated, mis-folded ) Knowledge of this structure is vital in understanding the function of the protein. For lack of better terms, structural information is usually classified as one of secondary, tertiary and quaternary structure. In Biochemistry and Structural biology, secondary structure is the general three-dimensional form of local segments of Biopolymers such as In Biochemistry and Chemistry, the tertiary structure of a Protein or any other Macromolecule is its three-dimensional structure as defined In Biochemistry, quaternary structure is the arrangement of multiple folded Protein molecules in a multi-subunit complex A viable general solution to such predictions remains an open problem. As of now, most efforts have been directed towards heuristics that work most of the time.

One of the key ideas in bioinformatics is the notion of homology. In Evolutionary biology, homology has come to mean any similarity between characters that is due to their shared ancestry. In the genomic branch of bioinformatics, homology is used to predict the function of a gene: if the sequence of gene A, whose function is known, is homologous to the sequence of gene B, whose function is unknown, one could infer that B may share A's function. In the structural branch of bioinformatics, homology is used to determine which parts of a protein are important in structure formation and interaction with other proteins. In a technique called homology modeling, this information is used to predict the structure of a protein once the structure of a homologous protein is known. This currently remains the only way to predict protein structures reliably.

One example of this is the similar protein homology between hemoglobin in humans and the hemoglobin in legumes (leghemoglobin). The oxygen carrier leghemoglobin (also legoglobin) is a Hemoprotein found in the nitrogen-fixing root nodules of leguminous plants Both serve the same purpose of transporting oxygen in the organism. Though both of these proteins have completely different amino acid sequences, their protein structures are virtually identical, which reflects their near identical purposes.

Other techniques for predicting protein structure include protein threading and de novo (from scratch) physics-based modeling.

See also structural motif and structural domain. In an unbranched chain-like biological Molecule, such as a Protein or a strand of RNA, a structural motif is a three-dimensional structural A protein domain is a part of protein sequence and structure that can evolve, function and exist independently of the rest of the protein chain

Comparative genomics

Main article: Comparative genomics

The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis) or other genomic features in different organisms. Comparative genomics is the study of the relationship of Genome structure and function across different biological Species or strains. History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance It is these intergenomic maps that make it possible to trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral transfer, inversion, transposition, deletion and insertion. Ultimately, whole genomes are involved in processes of hybridization, polyploidization and endosymbiosis, often leading to rapid speciation. An endosymbiont is any Organism that lives within the body or cells of another organism i The complexity of genome evolution poses many exciting challenges to developers of mathematical models and algorithms, who have recourse to a spectra of algorithmic, statistical and mathematical techniques, ranging from exact, heuristics, 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. heuristic (hyu̇-ˈris-tik is a method to help solve a problem commonly an informal method In Computer science and Operations research, approximation algorithms are Algorithms used to find approximate solutions to Optimization problems Bayesian inference is Statistical inference in which evidence or observations are used to update or to newly infer the Probability that a hypothesis may be true

Many of these studies are based on the homology detection and protein families computation.

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 the complex connections of these cellular processes. Systems biology is a biology-based inter-disciplinary study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective A computer simulation, a computer model or a computational model is a Computer program, or network of computers that attempts to simulate an The cell is the structural and functional unit of all known living Organisms It is the smallest unit of an organism that is classified as living and is often called A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Metabolism is the set of Chemical reactions that occur in living Organisms in order to maintain Life. In Biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another A Gene regulatory network (also called a GRN or genetic regulatory network) is a collection of DNA segments in a cell which interact with each Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms. Artificial life (commonly Alife or alife) is a field of study and an associated art form which examine Systems related to Life, its processes

High-throughput image analysis

Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery. Modern image analysis systems augment an observer's ability to make measurements from a large or complex set of images, by improving accuracy, objectivity, or speed. "n objective account is one which attempts to capture the nature of the object studied in a way that does not depend on any features of the particular subject who studies it A fully developed analysis system may completely replace the observer. Although these systems are not unique to biomedical imagery, biomedical imaging is becoming more important for both diagnostics and research. Some examples are:

• high-throughput and high-fidelity quantification and sub-cellular localization (high-content screening, cytohistopathology)
• 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

Protein-protein docking

Main article: Protein-protein docking

In the last two decades, tens of thousands of protein three-dimensional structures have been determined by X-ray crystallography and Protein nuclear magnetic resonance spectroscopy (protein NMR). High Content screening is an automated Cell biology method drawing on Optics, Chemistry, Biology and Image analysis to permit rapid Morphometrics is a field concerned with studying variation and change in the form (size and shape of organisms Commonly the measurements taken are of little significance in terms of X-ray crystallography is a method of determining the arrangement of Atoms within a Crystal, in which a beam of X-rays strikes a crystal and scatters Protein nuclear magnetic resonance spectroscopy (usually abbreviated protein NMR) is a field of Structural biology in which NMR spectroscopy is used One central question for the biological scientist is whether it is practical to predict possible protein-protein interactions only based on these 3D shapes, without doing protein-protein interaction experiments. Protein-protein interactions refer to the association of Protein molecules and the study of these associations from the perspective of Biochemistry, Signal transduction A variety of methods have been developed to tackle the Protein-protein docking problem, though it seems that there is still much place to work on in this field.

Software tools

Software tools for bioinformatics range from simple command-line tools, to more complex graphical programs and standalone web-services. The computational biology tool best-known among biologists is probably BLAST, an algorithm for determining the similarity of arbitrary sequences against other sequences, possibly from curated databases of protein or DNA sequences. In Bioinformatics, B asic L ocal A lignment S earch T ool or BLAST, is an Algorithm for comparing primary The NCBI provides a popular web-based implementation that searches their databases. The National Center for Biotechnology Information ( NCBI) is part of the United States National Library of Medicine (NLM a branch of the National Institutes BLAST is one of a number of generally available programs for doing sequence alignment. This list of sequence alignment software is a compilation of software tools and web portals used in pairwise Sequence alignment and Multiple sequence alignment.

SOAP-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, data and computing resources on servers in other parts of the world. SOAP (see below for name and origins is a protocol for exchanging XML -based messages over Computer networks normally using The availability of these SOAP-based bioinformatics web services through systems such as the BioMoby service register demonstrate the applicability of web based bioinformatics solutions. BioMOBY is a registry of Web services used in Bioinformatics. These tools range from a collection of standalone tools with a common data format under a single, standalone or web-based interface, to integrative and extensible bioinformatics workflow management systems. A bioinformatics workflow management system is a specialized form of Workflow management system designed specifically to compose and execute a series of computational or data

See also

Related topics

Related fields

Applied mathematics Artificial intelligence Biology Cheminformatics Clinomics Computational biology Computational epigenetics

Computational science Computer science Cybernetics Genomics Informatics Information theory Mathematical biology

Neuroinformatics Proteomics Scientific computing Statistics Structural biology Systems biology Theoretical biology

References

External links

• Major Organizations
  • Bioinformatics Organization (Bioinformatics.Org): The Open-Access Institute
  • EMBnet
  • European Bioinformatics Institute
  • European Molecular Biology Laboratory
  • The International Society for Computational Biology
  • National Center for Biotechnology Information
  • National Institutes of Health homepage
  • Open Bioinformatics Foundation: umbrella non-profit organization supporting certain open-source projects in bioinformatics
  • Swiss Institute of Bioinformatics
  • Wellcome Trust Sanger Institute

• Major Journals
  • Algorithms in Molecular Biology
  • Bioinformatics
  • BMC Bioinformatics
  • Briefings in Bioinformatics
  • Evolutionary Bioinformatics
  • Genome Research
  • The International Journal of Biostatistics
  • Journal of Computational Biology
  • Cancer Informatics
  • Journal of the Royal Society Interface
  • Molecular Systems Biology
  • PLoS Computational Biology
  • Statistical Applications in Genetic and Molecular Biology
  • Transactions on Computational Biology and Bioinformatics - IEEE/ACM
  • International Journal of Bioinformatics Research and Applications
  • List of Bioinformatics journals at Bioinformatics. The The Wellcome Trust Sanger Institute (formerly the Sanger Centre is a Genome research centre in the Wellcome Trust Genome Campus in Cambridgeshire, fr
  • EMBnet.News at EMBnet. org

• Other sites
  • The Collection of Biostatistics Research Archive
  • Human Genome Project and Bioinformatics
  • List of Bioinformatics Research Groups at Bioinformatics. fr
  • List of Bioinformatics Research Groups at the Open Directory Project

Genomics topics

Genome project | Paleopolyploidy | Glycomics | Human Genome Project | Proteomics | Metabolomics

Chemogenomics | Structural genomics | Pharmacogenetics | Pharmacogenomics | Toxicogenomics | Computational genomics

Bioinformatics | Cheminformatics | Systems biology

The Open Directory Project ( ODP) also known as dmoz (from directory Genomics is the study of an organism's entire Genome. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale Genetic Genome projects are Scientific endeavours that ultimately aim to determine the complete Genome sequence of an Organism (be it an Animal, a Paleopolyploidy refers to ancient Genome duplications which occurred at least several million years ago (mya Glycomics, an analogous term to Genomics and Proteomics, is the comprehensive study of Glycomes (the entire complement of Sugars whether free The Human Genome Project (HGP was an international Scientific research project with a primary goal to determine the sequence of chemical base pairs which make up DNA Proteomics is the large-scale study of Proteins particularly their structures and functions. Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" - specifically the study of their small-molecule metabolite Chemogenomics can be defined as the study of genomic responses to Chemical compounds The goal is the rapid identification of novel Drugs and Drug targets Structural genomics consists in the determination of the three dimensional structure of all Proteins of a given organism by experimental methods such as X-ray crystallography The terms Pharmacogenomics and pharmacogenetics tend to be used interchangeably and a precise consensus definition of either remains elusive Pharmacogenomics is the branch of Pharmacology which deals with the influence of genetic variation on drug response in patients by correlating Gene expression Toxicogenomics is a field of Science that deals with the collection interpretation and storage of information about gene and Protein activity within Computational genomics is the study of deciphering biology from Genome sequences using computational analysis Cheminformatics (also known as chemoinformatics and chemical informatics) is the use of computer and informational techniques applied to a range of problems Systems biology is a biology-based inter-disciplinary study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective

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