[Biopython] Monte Carlo Simulation

[Jeremias Ponciano da Silva]

Thanks Jared for the reply.
Seek a similarity of DNA, for example with the blast, getting this similar
sequence, eg 70%, I got to take this sequence, and do a test to see if it
is significant or not, making the randomization of this sample obtained, I
thought to do with Monte Carlo test to see if this within the normal 95% or
beyond 5%, which is what I seek.


2014/1/14 Jared Adolf-Bryfogle <jadolfbr at gmail.com>

> I think the distribution of your simulation will always be random - No
> monte carlo.  I'm not sure the problem your trying to solve.  If you want a
> monte carlo - based design algorithm on a structure, then you can try
> Rosetta:  https://www.rosettacommons.org/ (but I'm not sure if it does
> DNA design).
>
> Do you mean the combinations of sequences you get out?  Basically in
> either of these cases, the more times you choose a sequence, the more you
> sample the sequence space - however - your distribution will always be
> random, in that some sequences are not preferred.  Monte carlo is useful
> when you have a very large space to sample from, some constraints (such as
> a design algorithm and a dna structure), and you want to sample the range
> of possibilities.  In your case, you have no constraints, so,
> unfortunately, the result has no meaning...
>
> I would go back and see if Monte Carlo is what you really want?
>
>
> Jared Adolf-Bryfogle
> PhD Candidate
> Lab of Dr. Roland Dunbrack
> FCCC/DrexelMed
>
>
>
>
> On Tue, Jan 14, 2014 at 1:57 PM, Jeremias Ponciano da Silva <
> jere_2001 at ig.com.br> wrote:
>
>> Hi guys!
>> Thanks for the replies.
>> I can do randomization, even my biggest problem is how to make a plot of
>> Monte Carlo with the data I already have.
>>
>>
>> 2014/1/14 Michael Thon <mike.thon at gmail.com>
>>
>> > Check out:
>> >
>> >
>> http://stackoverflow.com/questions/976882/shuffling-a-list-of-objects-in-python
>> >
>> > Something like this should work:
>> >
>> > from random import shuffle
>> >
>> > x = ‘GCAT’
>> > s = list(x)
>> > shuffle(s)
>> >
>> >
>> > On Jan 14, 2014, at 4:04 AM, Jeremias Ponciano da Silva <
>> > jere_2001 at ig.com.br> wrote:
>> >
>> > > Hi people!
>> > > I'm doing a Monte Carlo Simulation, must take a DNA sequence and this
>> > > sequence can randomize N times, and with these seguencias plot on a
>> > Normal
>> > > chart monte carlo simulation, one would have any suggestions?
>> > >
>> > > --
>> > > *Jeremias Ponciano*
>> > > _______________________________________________
>> > > Biopython mailing list  -  Biopython at lists.open-bio.org
>> > > http://lists.open-bio.org/mailman/listinfo/biopython
>> >
>> >
>>
>>
>> --
>> *Jeremias Ponciano*
>>
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>
>


-- 
*Jeremias Ponciano*