The Molecular Biology Notebook Online
A Beginners' Guide to Molecular Biology

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Genetic

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Genetic Code; the DNA sequence of a gene can be used to predict the mRNA sequence, and in turn be used to predict the amino acid sequence of a polypeptide.

View Dr Chromo's lecture on 'The genetic code'.

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Related Links

This is a search for genetic in our database

• A Hypermedia Glossary of Genetic Terms: Glossary of genetic terms with pictures and links, results show also the context sensitive meaning of the related terms.
• A primer to phylogenetic analysis using Phylip package: The purpose of this tutorial is to demonstrate how to use Phylip, a collection of phylogenetic analysis software, and some of the options that are available. This tutorial is not intented to be a course in phylogenetics, although some phylogenetic concepts will be discussed briefly.
• AgBioTechNet: AgBiotechNet, the online service for agricultural biotechnology, delivers an exciting range of content on plant and animal biotechnology. It provides easy access to information on cloning, genomics, genetic engineering, in vitro culture, biosafety, intellectual property rights and all key issues in agricultural biotechnology through news, reviews, abstracts reports, links, book chapters and much more.
• All Species Inventory: If we discovered life on another planet, the first thing we would do is conduct a systematic inventory of that planet's life. This is something we have never done on our home planet. The aim of the All Species Inventory is simple: within the span of our own generation, record and genetically sample every living species of life on Earth.
• An Alphabetic List of Genetic Analysis Software: This list mainly contains computer software on genetic linkage analysis, marker mapping, and pedigree drawing.
• Arlequin 3.0: The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. The graphical interface is designed to allow users to rapidly select the different analyses they want to perform on their data. We felt important to be able to explore the data, to analyze several times the same data set from different perspectives, with different selected options. The statistical tests implemented in Arlequin have been chosen such as to minimize hidden assumptions and to be as powerful as possible. Thus, they often take the form of either permutation tests or exact tests, with some exceptions. Finally, we wanted Arlequin to be able to handle genetic data under many different forms, and to try to carry out the same types of analyses irrespective of the format of the data.
• Beadle, George Wells: ...they began the study of the development of eye pigment in Drosophila which later led to the work on the biochemistry of the genetics of the fungus Neurospora for which Beadle and Edward Lawrie Tatum were together awarded the 1958 Nobel Prize for Physiology or Medicine.
• Biology Project: Cell cycle and Mitosis tutorial: This exercise is designed to introduce you to the events that occur in the cell cycle and the process of mitosis that divides the duplicated genetic material creating two identical daughter cells
• BioMolecular Engineering Research Center: The BMERC is using and creating tools and methods for the study of computational biology. The center is working on secondary protein structure prediction, providing reliable profiles, and developing new ways to study molecular biology through Bioinformatics. Our work has led to the formulation and testing of major hypotheses in the areas of molecular evolution, gene regulation, developmental genetics, and protein structure-function relationships.
• Bioresearch online: Source for professionals in the bioresearch and life sciences industry- Information on drug discovery, laboratory systems and equipment, molecular and cell biology, genetic sequencing and more
• BioTech\\\'s life science dictionary: This free resource was developed by our staff members and contributors and is still very much under construction. Currently, most of our 8300+ terms deal with biochemistry, biotechnology, botany, cell biology and genetics.
• CEPH-Genethon genetic map data: Genetic map data for chromosomes.
• ChromDB: The Plant Chromatin Database: The mission of ChromDB is to bring together information on homologs of chromatin-associated proteins encoded by plant genomes, organize this information logically and in a comparative manner across species (with reference to other eukaryotes to the extent possible), and make it readily accessible to any members of the research and teaching communities who might be interested in the role played by chromatin proteins in the control of gene expression and genome organization. Our first priority is to provide (a) complete sets of genes encoding chromatin-associated proteins (CAPs) for those plant species with complete or near-complete genome sequences (currently Arabidopsis and rice, with poplar to be displayed in the future), (b) the best available splicing models and predicted protein sequences for these genes, and (c) a molecular phylogenetic context for understanding the evolutionary diversification of these protein families during plant evolution with reference to animal and fungal homologs. Our next priorities will be to identify and present CAP genes in all available EST and partial genomic sequences of other plant species, as well as to provide information regarding their biochemical, developmental, physiological, and cellular functions through a community annotation mechanism.
• Computational Genomic Group (CGG): Computational approaches for analysis of nucleotide and protein sequences and structures as well as understanding structural and functional organization of genetic signals encoded in genome sequences.
• Cystic Fibrosis Gene location on chromosome 7: The OMIM map presents the cytogenetic map location of disease genes and other expressed genes described in OMIM.
• Cystic Fibrosis Mutation Database: The information contained in this database is compiled with information collected by the Cystic Fibrosis Genetic Analysis Consortium.
• Data Analysis Software from the BRC: The following software for genetic data analysis were developed and made available by researchers at or affiliated with the Bioinformatics Research Center:
  • Alternative Splicing Gallery (ASG)
  • GDA
  • QTL Cartographer
  • Windows QTL Cartographer
  • Forensic DNA Mixtures
  • Hy-Phy
  • PowerMarker
  • Mixed Models and QTLs
  • Exact Tests
  • Cytonuclear Disequilibria
• Delbrück, Max: Discoveries concerning the replication mechanism and the genetic structure of viruses..
• Edinburg Pathway Editor: EPE is a visual editor designed for annotation, visualisation and presentation of wide variety of biological networks, including metabolic, genetic and signal transduction pathways. It based on a metadata driven architecture, which makes it very flexible in drawing, storing, presenting and exporting information related to the network of interest. It allows visual representation to field standards (SBGN), storage and retrieval of annotation such as kinetic and other numerical data in relational databases (local and remote for enterprise development) and links graphical objects to external databases and web resources to show all available information on demand.
• Expressed Sequence Tags (dEST): dbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or Expressed Sequence Tags, from a number of organisms. A brief account of the history and current status of human ESTs in GenBank is available (Trends Biochem. Sci. 20:295-6;1995). Also, consult the special "Genome Directory" issue of Nature (vol. 377, issue 6547S, 28 September 1995).
• fastDNAml construction of phylogenetic trees of DNA Sequences: References:
  Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48.
  Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.
  
• FigTree: FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.
• Flybase: FlyBase is a database of genetic and molecular data for Drosophila. It is available through FlyBase servers, as partial mirrors on other servers, as flat files, and as printed text (in special issues of Drosophila Information Service). The full database includes data files, documents, indices, forms, and images and is maintained on a multi-protocol server that supports a variety of tools and formats.
• FreeTree:  Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites, by V. Hampl, A. Pavlicek and J. Flegr
• GenBank: GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences ( Nucleic Acids Research 1998 Jan 1;26(1):1-7). There are approximately 1,622,000,000 bases in 2,356,000 sequence records as of June 1998. As an example, you may view the record for the neurofibromatosis gene.
• GeneSpring: cutting-edge tools for expression analysis: GeneSpring is widely regarded as the gold standard for expression data analysis. When you use GeneSpring, you join thousands of elite scientists worldwide who depend on its sophisticated analysis techniques to advance their research. Designed to meet the needs of the individual researcher, GeneSpring seamlessly interfaces with Silicon Genetics’ Signet software, which provides a highly scalable platform for enterprise- level genomic research
• Genetic Education Center: For educators interested in human genetics and the human genome project.
• Genetic Programming Notebook: Genetic programming is a branch of genetic algorithms. The main difference between genetic programming and genetic algorithms is the representation of the solution. Genetic programming creates computer programs in the lisp or scheme computer languages as the solution. Genetic algorithms create a string of numbers that represent the solution.
• Genetics Forum: The Genetics Forum is the only independent organisation in the UK concerned with the use of new genetic technologies and their public policy implications. It was founded in 1989 by a group of scientists, lawyers and advocates from the animal welfare, environmental and consumer movements concerned about the long-term impact of rapid developments in the genetic sciences.
• Hershey, Alferd Day: Nobel prize in 1969 for their discoveries concerning the replication mechanism and the genetic structure of viruses
• Human Genome Project: The Human Genome Project (HGP) was one of the great feats of exploration in history - an inward voyage of discovery rather than an outward exploration of the planet or the cosmos; an international research effort to sequence and map all of the genes - together known as the genome - of members of our species, Homo sapiens. Completed in April 2003, the HGP gave us the ability to, for the first time, to read nature\'s complete genetic blueprint for building a human being.
• IMGT - International ImMunoGeneTics Database: IMGT, the international ImMunoGeneTics database, is a high-quality integrated database specialising in Immunoglobulins (Ig), T-cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species. IMGT includes two databases : LIGM-DB, a comprehensive database of Ig and TcR from human and other vertebrates and MHC/HLA-DB (in development). A tool, IMGT/DNAPLOT, will allow Ig, TcR and MHC sequence analysis.
• IMGT, international ImMunoGeneTics database: IMGT, the international ImMunoGeneTics database, is a high-quality integrated database specialising in Immunoglobulins (Ig), T cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species, created in 1989 by Marie-Paule Lefranc (Université Montpellier II, CNRS). IMGT, a European project since 1992, works in close collaboration with EBI.
• Jacob, Francois: The work of François Jacob has dealt mainly with the genetic mechanisms existing in bacteria and bacteriophages, and with the biochemical effects of mutations.
• MAC5: MAC5 is a program which implements MCMC sampling to estimate a phylogenetic tree from a DNA multiple alignment. What differentiates MAC5 from similar programs (e.g. BAMBE, MrBayes) is its use of five-state sequence evolution models as a means to include the gap information when estimating an alignment. Despite vilification of these models in the literature in the past (e.g., Durbin et al., 1998, p. 217), we have found that, in many circumstances, they are useful for improving the precision of topology estimation.
• Marine Ecology Research Group: You will find here some information on
  
• Ecological Genetics of Parasitic Sea Lice
• Inducible Morphology in Marine Bryozoans
• Larval Dispersal
• Biofilms and Larval Settlement
• Mega: the goal of the MEGA (Molecular Evolutionary Genetics Analysis) software project has been to make useful methods of comparative sequence analysis easily accessible to the scientific community for research and education.
• Mendel Web: MendelWeb is an educational resource for teachers and students interested in the origins of classical genetics, introductory data analysis, elementary plant science, and the history and literature of science.
• Molecular Biology Gateway: The ultimate gateway to Web resources for molecular biology, genetics, microbiology, and biochemistry
• Molecular Genetics: The objectives of the course were, and continue to be: to train students to interpret experimental observations in molecular genetics; to have students understand the experimental bases for molecular genetic principles; and to train students to apply experimental methods of molecular genetics to problems in that science. These objective have been shaped by my philosophy of teaching science. I believe it more important that students learn why we believe the things we believe about molecular genetics than to memorize current hypotheses of the the science.
• Molecular Genetics: Chromosomes: The three conceptual types of chromosomes, their interrelation and inheritance.
  
  The objectives of the course were, and continue to be: -to train students to interpret experimental observations in molecular genetics;
  -to have students understand the experimental bases for molecular genetic principles; and
  to train students to apply experimental methods of molecular genetics to problems in that science.
• Monod, Jacques Lucien: To George Teissier he owes a preference for quantitative descriptions; André Lwoff initiated him into the potentials of microbiology; to Boris Ephrussi he owes the discovery of physiological genetics, and to Louis Rapkine the concept that only chemical and molecular descriptions could provide a complete interpretation of the function of living organisms.
• MrEnt: MrEnt is a program for drawing high-quality, printable phylogenetic trees. It is a user-friendly software that recognizes Nexus tree files (like those generated by e.g. PAUP and MrBayes) and displays them in the most commonly used tree formats. Our goal was to produce a software to generate with no troubles all tree drawings for scientific publications directly from analysis outputs, without using any additional graphic editor.
• NJPlot: NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
• OMIM: Inheritance in Man - A catalog of human genes and genetic disorders.: Welcome to OMIM(TM), Online Mendelian Inheritance in Man. This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information.
• OmniMapFree: OmniMapFree is a computer program for displaying and analysing the genome of any organism. You can use it to generate genome maps of your own favourite organism and to link chromosome, genetic, transcriptomic, proteomic, molecular mutant and many other types of important information directly to the genomic sequence. It is very easy to use - it does not require any knowledge of databases or computer programming. All of the data is held in plain text files which can be created and modified using a simple text editor e.g. Notepad or Wordpad.
• On Gaps: Gonzalo Giribet andWard C. Wheeler, Molecular Phylogenetics and Evolution Vol. 13, No. 1, October, pp. 132–143, 1999
• ORf finder: This tool identifies all open reading frames using the standard or alternative genetic codes. The deduced amino acid sequence can be saved in various formats and searched against the sequence database using the WWW BLAST server.
• PALI Phylogeny and ALIgnment of homologous protein structures: This database provides structure based sequence alignments for homologous proteins of known 3-D structure. The alignments available include those of pairwise (two proteins at a time) and multiple (simultaneous superposition of all the structures in a family). The database also provides dendrograms depicting phylogenetic relationships based on sequence and structural similarities.
• Paper on FreeTree - tree computation program: It was originally intended for the analysis of results of DNA fingerprinting methods (RFLP, RAPD, AP-PCR) or other methods which provide binary character data (presence/absence of the characters). For such data the program computes the distance matrix, constructs the phylogenetic or phenetic tree and computes bootstrapping or jackknifing values for internal branches of the tree.
• Philodendron - Phylogenetic tree printer: Phylodendron is an application for drawing phylogenetic trees, used in evolutionary biology. Options allow you to save in various formats, print, edit, modify, and adorn the tree. This version of Phylodendron includes the ability to run as a Web service.
• Phylemon: a suite of web-tools for molecular evolution, phylogenetics and phylogenomics
• Phylogenetic Resources: Today\\\'s session is a VERY brief introduction to phylogenetics. For a more complete experience, consider the two week course, Workshop on Molecular Evolution held by the Marine Biological Laboratory at Woods Hole.
• PhylOgenetic Web Repeater (POWER): The PhylOgenetic Web Repeater (POWER) allows users performing phylogenetic analysis with molecular data by most programs of PHYLIP package repeatedly. POWER provide two pipelines to process the analysis. One of them includes multiple sequence alignment (MSA) at the begining of the pipeline whereas the other begin phylogenetic analysis with aligned sequence.
• Phylogeny and Reconstructing Phylogenetic Trees: These few pages describe the problem of reconstructing phylogenetic trees with the help of a Java applet. I wrote the applet to discover more about the java language and the API interface. I\'ve been interested in phylogenetic trees for some time and thought they would make a good subject. -- Dave Joyce
• PHYLOGENY ESTIMATION : traditional and Bayesian approaches: The construction of evolutionary trees is now a standard part of exploratory sequence analysis. Bayesian methods for estimating trees have recently been proposed as a faster method of incorporating the power of complex statistical models into the process. Researchers who rely on comparative analyses need to understand the theoretical and practical motivations that underlie these new techniques, and how they differ from previous methods. The ability of the new approaches to address previously intractable questions is making phylogenetic analysis an essential tool in an increasing number of areas of genetic research.
• Phylogeny for the faint of heart: A review from trends in Genetics that explains tree inference..
• Phylogeny.fr: Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences.
  
  Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences.
• Phyml at Phylogeny.fr: Robust Phylogenetic Analysis For The Non-Specialist
• POPGENE: The User-friendly Freeware For Population Genetic Analysis
• Population Biology Simulation: Collected here are a few simple simulations (written in Java) I use (or plan to use) when teaching principles of population genetics and population ecology in various courses. (Kent Holsinger)
• Populations to Molecules: 994 High School Biology Institute Faculty and Participants I. Historical Background Unraveling the Code of Life - A Historical Perspective of the Genetic Revolution History of Genetics Timeline
• Primer on Molecular Genetics: Primer on Molecular Genetics
• Primer3: Primer3 is a widely used program for designing PCR primers (PCR = Polymerase Chain Reaction). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers. PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals.
• Ribosomal Database Project: The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences
• Rothamsted Research: Over its 160 year history, Rothamsted Research has built an enviable international reputation as a centre of excellence for science in support of sustainable land management and its environmental impact. Its scientific research ranges from studies of genetics, biochemistry, cell biology and soil processes to investigations at the ecosystem and landscape scale.
• Saccharomyces genome database: SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
• Scottish Crop Research Institute: SCRI aims to increase knowledge in the basic biological sciences; to improve crop quality and utilisation by the application of conventional and molecular genetical techniques and novel agronomic practices; and to develop environmentally benign methods of protecting crops from depredations by pests, pathogens and weeds.
• Software for the Analysis of RAPD Data Sets: I have cobbled this page together in an attempt to inform other researchers of programs that are available from the web to assist in the analysis of genetic data acquired from RAPD-PCR.
• Spanish Omelette: analogy to fundamental dogma: The following is a good way to show the relationships among cell, nucleus, genes, chromosome, ribosome, replication, mitosis, transcription, translation, DNA, RNA, amino acids and proteins, genotype, phenotype, and genetic vs. environmental causes of cell defects.
• Tatum, Edward Laurie: ...when he and Beadle decided to give up their work on Drosophila and to work instead with the fungus Neurospora crassa, it was Tatum who discovered that biotin was necessary for the successful cultivation of this fungus on simple inorganic media and thus provided these two workers with the genetic material that they needed for the work which gained them, together with Joshua Lederberg, the Nobel Prize.
• Technical Tips Online: Technical Tips Online is a new electronic publication forum that builds on the success and popularity of the Technical Tips section in Trends in Genetics. It is available free of charge to all users.
• The DNA Files: The genetic revolution affects us every day: our health, our food, our families. The DNA Files explains how.
• The Gene School: a comprehensive, educational site exploring the fascinating innovations and discoveries of genetic science. Begin your journey through the world of genetics using the search engine or simply by browsing through a topic; either way, you will find that genetic science is an exciting field!
• The Tech Genetics: Understanding Genetics, the newest online exhibition from TheTech Museum.
• TOPALi: There are a growing number of biological questions that can be answered by analysing multiple sequence alignment data. We have extended the original TOPALi Java application, beyond recombination detection, to launch a range of statistical and evolutionary analyses of multiple sequence alignments as web services. The extended TOPALi v2 provides phylogenetic model selection, Bayesian analysis (BA) and Maximum Likelihood (ML) phylogenetic tree estimation, detection of sites under positive selection, and recombination breakpoint location analysis.
• TOPD/FMTS : TOPD/FMTS is a new software for comparing phylogenetic trees. It has been developed to calculate the differences between trees. The software implements several previously described methods and new algorithms for comparing phylogenetic trees. It combines the TOPD program (TOPological Distance), which compares two trees with the same taxa or two pruned trees, and the FMTS program (From Multiple To Single), which converts multi-gene family trees to single-gene trees.
• Tree inference at the T-REX server: The most comprehensive web server version includes methods for Visualization and interactive manipulation of phylogenetic trees (using Hierarchical, Radial and Axial types of drawing); Inference of phylogenetic trees using distance (NJ, BioNJ, UNJ, ADDTREE, MW, FITCH, Circular order reconstruction),parsimony (DNAPARS, PROTPARS, PARS, DOLLOP) and maximum likelihood (PHYML, DNAML, DNAMLK, PROML, PROMLK) based approaches; Inference of phylogenetic trees form incomplete distance matrices; Inference of phylogenetic networks (i.e. Reticulograms); Detection of horizontal gene transfers; Multiple sequence alignment (ClustalW), Sequence to distance transformations(using Uncorrected, Jukes-Cantor, Tajima-Nei, Kimura 2-parameter, Tamura, Jin-Nei gamma, Kimura protein, LogDet and F84 distances); Computation of the Robison and Foulds topological distance between two or more trees. The program can also carry out bootstrap and jackknife resampling to assess strength of support of the tree and network branches.
• TreeBase: TreeBASE stores phylogenetic trees and the data matrices used to generate them from published research papers.
• TreeGraph 2: TreeGraph 2 is a graphical editor for phylogenetic trees which allows you to apply lots of graphical formats to the elements of your tree. Moreover, it supports several (visible or invisible) annotations (e.g. support values) for every branch or node. These annotations can be imported from Nexus tree files or text files containing data in a table (e.g. exported from a spreadsheet program).
• Tribolium Home Page: This site contains data and articles about the genetics of the red flour beetle, Tribolium castaneum, and related species. Work being done in Dr. Beeman's laboratory involves both standard and molecular approaches.
• Tritimed: This project aims to identify crop traits and genetic ideotypes, in wheat, that impart higher and more stable yield under Mediterranean drought conditions. This shall be realised by using an integrated approach combing genomics, quantitative genetics and crop physiology
• Tutorial for Clustal X and TreeView: The Clustal programs are the choice for the novice to make a decent phylogenetic analysis of obtained nucleotide or amino acid sequences. Clustal can align the sequences and produce output files for drawing trees. The tree viewing feature is however not included in the standard Clustal packages.
• UGENE - Unipro: UGENE is a free cross-platform genome analysis suite. Multiple sequence alignment using MUSCLE 3,4 and KAlign; HMM profiles build and search, based on the source of HMMER 2 and HMMER 3; PCR Primers design using Primer 3; Protein secondary structure prediction using GOR IV and PSIPRED; Phylogenetic analysis with Phylip; Search for restriction enzymes and integration with REBASE; Extremely fast repeat finder; DNA reference assembly using Bowtie; Search for transcription factor binding sites using SITECON; Protein back translation; ORF finder; Complete Smith-Waterman algorithm implementation; Comparing genomes using dotplot view.

genetic on Wikipedia

genetic at Answers. com

New Links

-AIGO: Analysis and Intercomparison of Gene Ontology functional annotations
AIGO is a Python library for the Analysis and Inter-comparison of Gene Ontology (GO) functional anno...
-OmniMapFree
OmniMapFree is a computer program for displaying and analysing the genome of any organism. You can u...

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Copyright Rothamsted Research 1999- 2010
Web technical : Nathalie Castells-Brooke

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