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    • #16238
      softblackstars
      Participant

      i want to write a program about six-frames translation for dna sequences, who can help me to explain what is six-frames translation?

      thanks a lot.

    • #110198
      genetherapy
      Participant

      I didn’t understand what you mean. Can it be releated to the following ?:
      "We know that there are six possible reading frames for any given nucleotide sequence. Generally the longests Open reading frame is taken to be the correct frame, when we do not have information about the possible protein that is encoded by a given gene. By default the translate method performs translation in the first frame but it can take an argument that defines the translation frame" http://biorelated.com/2011/02/02/transl … h-bioruby/

    • #110202
      JackBean
      Participant

      So you want to make some program for something about what you have no idea what is it?

      hopefully, you know, that amino acids are coded by triplets, right? So for sequence ACTGACACAAGTTGACA
      the reading could be
      ACT GAC ACA AGT TGA CA

      but if we skip the first nucleotide (realize, that in DNA there are milions of nucleotides, so one nucleotide doesn’t really matter!), we will get this
      A CTG ACA CAA GTT GAC A
      something completely different, right? (you can try to translate it with the table)

      but if we skip yet other nt, we will get this
      AC TGA CAC AAG TTG ACA
      another new version!

      after skipping the next nucleotide we get
      ACT GAC ACA AGT TGA CA
      hey, but that’s the same as the first time! So, we get three different versions from one strand of DNA. But! the DNA is double stranded, and you can hardly predict which strand is the right one. Thus, you would do the same for reverse complement sequence and get 3*2 = 6 reading frames.

      Usage? As genetherapy wrote, when you do not know, which reading frame is the right one (e.g. for screening of EST), you will want to cover all of them.

    • #110237
      softblackstars
      Participant

      thanks a lot, that is what i mean.

      in fact, i want to write a small proram code about that.

    • #115468
      progistar
      Participant

      Wow! There is amazing teacher! I’ve ever seen those easy explanation ^-^.

      thanks a lot both softblackstars and JackBean!

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