what is six-frames translation

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softblackstars
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what is six-frames translation

Post by softblackstars » Mon Mar 19, 2012 9:11 am

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.

genetherapy
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Post by genetherapy » Mon Mar 19, 2012 12:47 pm

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/

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JackBean
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Post by JackBean » Mon Mar 19, 2012 1:33 pm

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.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.

softblackstars
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Re: what is six-frames translation

Post by softblackstars » Wed Mar 21, 2012 5:51 pm

thanks a lot, that is what i mean.

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

progistar
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Post by progistar » Tue Sep 30, 2014 2:12 pm

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

thanks a lot both softblackstars and JackBean!

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