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Online Artificial Gene Design

Posted by ryuzaki0 on from the outdated-already dept.

massivefoot writes to tell us New Scientist is reporting that researchers at Johns Hopkins University School of Medicine have released a new software suite, GeneDesign, that helps to simplify the steps in designing artificial DNA. From the article: "These key steps include translating proteins and amino acids - the building blocks which make proteins - backwards into a DNA sequence. Or the software can manipulate simulated DNA "codons" which can code for an amino acid. DNA codons are made of sets of three nucleotides - the fundamental molecules which link together to form a DNA chain."

8 of 100 comments (clear)

  1. For those who care by xirtap · · Score: 5, Informative

    Here is a link to GeneDesign: http://slam.bs.jhmi.edu/gd/

    1. Re:For those who care by RDW · · Score: 4, Informative

      ...or for serious work, check out EMBOSS, an open source collection of hundreds of molecular biology tools with a range of optional GUIs, including an excellent web interface available at multiple sites.

  2. It's one of those websites.... by technoextreme · · Score: 2, Informative
    Here is a link to GeneDesign: http://slam.bs.jhmi.edu/gd/
    That even if I rtfm I have no clue what's going on.
    --
    Ooo man the floppy drive is broken. No wait. The computer is just upside down.
  3. Re:Will the source code be available? by Anonymous Coward · · Score: 1, Informative

    Source code -> http://slam.bs.jhmi.edu/gd/source/ (at the bottom of the GeneDesign page)

  4. Re:Will the source code be available? by Quirk · · Score: 3, Informative

    Source code

    --
    "Academicians are more likely to share each other's toothbrush than each other's nomenclature."
    Cohen
  5. Old news again. by Lhooqtoo · · Score: 2, Informative

    Based on what I saw in the article, there's nothing this DNA does that hasn't been available in any number of DNA sequence manipulation suites for the last 10 years. 'Reverse translation', constructing a DNA sequence that could be transcribed and translated into actual protein is the sort of thing you might see in an undergraduate genetics homework assignment. Higher throughput versions, akin to what this article is describing, perhaps a masters level bioinformatics project. As to 'protecting' against potential evil-doers ordering proteins of mass destruction, viruses are quite a bit more complicated than proteins. Anyone who needs to order their custom gene from somebody else is not likely to be decades ahead of state of the art infectious disease researchers who, to the best of my knowledge, have been unable to generate a de novo infectious agent. Honestly, these algorithms have been around for quite some time.

  6. I'll stick to SMS2 by Henge · · Score: 2, Informative

    At first blush, GeneDesign 2.0 offers nothing over the long-available, free, web-based or local-mirrorable Sequence Manipulation Suite 2 at http://bioinformatics.org/sms2/. When I start on a molecular bio project, I use a mix of SMS2, BLAST, NEB cutter, IDT's web-tools, and other free online tools to accomplish everything I need, and keep track of my thought process in a simple Word document. This suite adds no functionality I don't have free access to already elsewhere.

  7. Re:Great progress (im affected) by Anonymous Coward · · Score: 1, Informative

    Because he spelled 3 words wrong and posted AC about dying.