Information & explanations, latest texts & monographs on
Bioinformatics (including recent related patents.)
BioinformaticsGenomics Genome project Glycomics Human Genome Project Proteomics Structural genomics Bioinformatics Systems biology Bioinformatics 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 is the data mining and analysis of the data gathered by the various genome projects. Other areas are sequence alignment, protein structure prediction, systems biology, and virtual evolution. As a summary, the various genome projects produce many long lists of letters and one of the roles of bioinformatics is to attempt to determine the words, grammar, sentences and ultimately, meaning (functional significance) of those letters. Table of contents showTocToggle("show","hide") 1 Sequence analysis 2 Bioinformatics tools 3 Bioinformatics and structural biology 4 Modeling biological systems 5 Other applications 6 Further information 6.1 See also 6.2 Related fields 6.3 References 6.4 External links Sequence analysis Main articles: Sequence alignment, Sequence database Since the Epstein-Barr virus was sequenced in 1984, the DNA sequence of more and more organisms is stored in electronic databases. This data is analyzed to determine genes that code for proteins, as well as regulatory sequences. 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). With the growing amount of data, it becomes impossible to analyze DNA sequences manually. Today, computer programs are used to find similar sequences in the genome of dozens of organisms, within billions of nucleotides. These programs can 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. The so-called shotgun sequencing (that was used, for example, by Celera Genomics to sequence the human genome) does not give a sequential list of nucleotides, but instead the sequences of thousands of small DNA fragments (each about 600 nucleotides long). The ends of these fragments overlap and, aligned in the right way, make up the complete genome. Shotgun sequencing yields sequence data quickly, but the task to re-align the fragments can be quite complicated for larger genomes. In the case of the Human Genome Project, it took several months on a supercomputer array to align them correctly. Shotgun sequencing is generally preferred for smaller genomes, such as bacteria, and often used at least partially on organisms with much larger genomes. DNA 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 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. Bioinformatics helps to bridge the gap between genome and proteome projects, for example in the use of DNA sequence for protein identification. Bioinformatics tools 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 BioPerl, BioPython, BioRuby, and BioJava which develop and distribute shared programming tools and objects (as program modules) that make bioinformatics easier. Bioinformatics and structural biology Main article: Protein structure prediction Protein structure prediction is another important application of bioinformatics. 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. But, the protein can 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 sequence is 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 of which the function is known, it is likely to have a similar function. In the structural branch of bioinformatics homology is used to determine which parts of the protein are important in structure formation and interaction with other proteins. In a technique called homology modelling, 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. Modeling biological systems 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. Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms. Other applications Morphometrics is used to analyze pictures of embryos to track and to predict the fate of cell clusters during morphogenesis. Further information See also
This article is adapted from from Wikipedia All Wikipedia article text is available under the terms of the GNU Free Documentation License Bioinformatics for Dummies by Jean-Michel Claverie Developing Bioinformatics Computer Skills by Cynthia Gibas Beginning Perl for Bioinformatics by James Tisdall Bioinformatics: Sequence and Genome Analysis by David W. Mount Mastering Perl for Bioinformatics by James D. Tisdall A Primer of Genome Science by Greg Gibson Bioinformatics Computing by Bryan Bergeron Fundamental Concepts of Bioinformatics by Dan E. Krane Introduction to Bioinformatics by Arthur M. Lesk Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition by Andreas D. Baxevanis Digital Code of Life : How Bioinformatics is Revolutionizing Science, Medicine and Business by Glyn Moody Structural Bioinformatics by Philip E. Bourne R for Bioinformatics by Kim Seefeld Biomedia (Electronic Mediations, V. 11) by Eugene Thacker Discovering Genomics, Proteomics, and Bioinformatics by A. Malcolm Campbell Recent Bioinformatics related patents From USPTO: 6716636: Methods for sequencing proteins 6716588: System for cell-based screening 6716582: Cellular arrays for the identification of altered gene expression 6714925: System for identifying patterns in biological data using a distributed network 6713260: Methods of identifying compounds that bind to target species under isothermal denaturing conditions 6710229: Cell cycle stress-related proteins and methods of use in plants 6710170: Compositions and methods for the therapy and diagnosis of ovarian cancer 6709840: Anergy associated genes 6707539: Portable product authentication device 6706867: DNA array sequence selection 6706711: Pyrazole derived kinase inhibitor 6706685: Compounds and methods for stimulating .beta.-catenin mediated gene expression and differentiation 6706529: Methods for sequencing proteins 6706513: Adenosine deaminase homolog 6706501: Polynucleotide encoding a propionibacterium linoleate isomerase and uses thereof 6706485: Method of identifying agents that inhibit APP processing activity 6706262: Compounds and methods for therapy and diagnosis of lung cancer 6703491: Drosophila sequences 6703224: Zcys6: a member of the cystatin superfamily 6703223: Nucleotide sequences coding for the MtrA and/or MtrB proteins 6703020: Antibody conjugate methods for selectively inhibiting VEGF 6701254: Method for analyzing samples of biomolecules in an array 6699865: Pyrazole compositions useful as inhibitors of ERK 6699704: Heat tolerant phytases 6699671: Alzheimer's disease secretase, APP substrates therefor, and uses therefor 6699670: Quantitative assay for the simultaneous detection and speciation of bacterial infections 6699664: Compositions and methods for the therapy and diagnosis of ovarian cancer 6696620: Immunoglobulin binding protein arrays in eukaryotic cells 6696619: Plant aminoacyl-tRNA synthetases 6696454: Inhibitors of spermidine synthase for the treatment of osteoarthritis and cartilage rehabilitation 6696292: Genes encoding sulfate assimilation proteins 6696247: Compounds and methods for therapy and diagnosis of lung cancer 6696239: Comparative phenotype analysis for assessment of biological active compounds such as antimicrobials 6693186: Neisseria meningitidis polypeptide, nucleic acid sequence and uses thereof 6692946: Polynucleotides encoding the nadA gene and methods of producing nicotinic acid or nicotinic acid derivatives 6692936: Nucleic acid encoding a C5A anaphylatoxin receptor 6692916: Systems and methods for characterizing a biological condition or agent using precision gene expression profiles 6692748: Adipocyte complement related protein zacrp3x2 and nucleic acids encoding zacrp3x2 6691109: Method and apparatus for high-performance sequence comparison 6689939: GTP binding stress-related proteins and methods of use in plants 6689601: High growth methanotropic bacterial strain 6689570: Methods of identifying agents which bind GPR-9-6 6687692: Method and apparatus for providing an expression data mining database 6686447: Compositions and methods for the therapy and diagnosis of lung cancer 6686188: Polynucleotide encoding a human myosin-like polypeptide expressed predominantly in heart and muscle 6683173: Tm leveling methods 6683169: Nucleic acid encoding the human peptide histidine transporter 1 and methods of use thereof 6682942: Microdevices for screening biomolecules 6682923: Thermostable alkaliphilic xylanase |
