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Gene Designer
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Encyclopedia
Gene Designer is a free bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

 software package. It is used by Molecular Biologists
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...

 from academia, government and the pharmaceutical, chemical, agricultural and biotechnology industries to design, clone and validate genetic sequences.

Features

Gene Designer enables Molecular Biologists to capture the entire gene design process in one application, using a range of design tools.
  • Algorithms for in silico
    In silico
    In silico is an expression used to mean "performed on computer or via computer simulation." The phrase was coined in 1989 as an analogy to the Latin phrases in vivo and in vitro which are commonly used in biology and refer to experiments done in living organisms and outside of living organisms,...

     cloning
    Molecular cloning
    Molecular cloning refers to a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and to direct their replication within host organisms...

    , codon optimization
    Codon usage bias
    Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation .There are 64 different codons but only 20...

    , back translation
    Translation (genetics)
    In molecular biology and genetics, translation is the third stage of protein biosynthesis . In translation, messenger RNA produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein...

     and Primer Design
  • Graphic Molecular View to display, annotate and edit constructs
  • Customizable database to store, manage and track genetic elements, Genes
    Gênes
    Gênes is the name of a département of the First French Empire in present Italy, named after the city of Genoa. It was formed in 1805, when Napoleon Bonaparte occupied the Republic of Genoa. Its capital was Genoa, and it was divided in the arrondissements of Genoa, Bobbio, Novi Ligure, Tortona and...

     and constructs
  • Drag-and-Drop interface for moving sequence elements within or between constructs
  • Search feature for Sequence motif
    Sequence motif
    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 significance...

    s, Restriction sites and Open reading frame
    Open reading frame
    In molecular genetics, an open reading frame is a DNA sequence that does not contain a stop codon in a given reading frame.Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop...

    s.
  • Codon optimize for recombinant protein expression
    Protein expression
    Protein expression is a subcomponent of gene expression. It consists of the stages after DNA has been translated into polypeptide chains, which are ultimately folded into proteins...

     in any organism using multiple algorithms.
  • Remove or add Restriction sites or other Sequence motif
    Sequence motif
    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 significance...

    s
  • Recode Open reading frames
  • Check translation frames
    Translation (genetics)
    In molecular biology and genetics, translation is the third stage of protein biosynthesis . In translation, messenger RNA produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein...

     and fusion junctions
  • Design Oligonucleotide
    Oligonucleotide
    An oligonucleotide is a short nucleic acid polymer, typically with fifty or fewer bases. Although they can be formed by bond cleavage of longer segments, they are now more commonly synthesized, in a sequence-specific manner, from individual nucleoside phosphoramidites...

    s for sequencing primers
    Primer (molecular biology)
    A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. They are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA...

    , includes a real time melting point calculator
  • Cloning Tool with drag-and-drop ability to cut, combine and clone
    Molecular cloning
    Molecular cloning refers to a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and to direct their replication within host organisms...

     insert and vector
    Vector (molecular biology)
    In molecular biology, a vector is a DNA molecule used as a vehicle to transfer foreign genetic material into another cell. The four major types of vectors are plasmids, viruses, cosmids, and artificial chromosomes...

    .

See also

  • Bioinformatics
    Bioinformatics
    Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

  • Computational biology
    Computational biology
    Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems...

  • Gene synthesis
    Gene synthesis
    Artificial gene synthesis is the process of synthesizing a gene in vitro without the need for initial template DNA samples. The main method is currently by oligonucleotide synthesis from digital genetic sequences and subsequent annealing of the resultant fragments...

  • Vector (molecular biology)
    Vector (molecular biology)
    In molecular biology, a vector is a DNA molecule used as a vehicle to transfer foreign genetic material into another cell. The four major types of vectors are plasmids, viruses, cosmids, and artificial chromosomes...

    , Vector DNA, Cloning vector
    Cloning vector
    A cloning vector is a small piece of DNA into which a foreign DNA fragment can be inserted. The insertion of the fragment into the cloning vector is carried out by treating the vehicle and the foreign DNA with a restriction enzyme that creates the same overhang, then ligating the fragments...

    , Expression vector
    Expression vector
    An expression vector, otherwise known as an expression construct, is generally a plasmid that is used to introduce a specific gene into a target cell. Once the expression vector is inside the cell, the protein that is encoded by the gene is produced by the cellular-transcription and translation...

  • Restriction map
  • Molecular cloning
    Molecular cloning
    Molecular cloning refers to a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and to direct their replication within host organisms...

  • List of open source bioinformatics software

Educator and Student Use

This free software has been incorporated into Synthetic Biology, Systems Biology, Bioengineering and BioInformatics classroom and lab curricula. Students create and complete projects which capture the entire gene design process in one application, using a range of design tools.

Examples of use in Curricula:

External links

Description of software

Tutorials

Other Software

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