[BiO BB] Random Sequence Generator

[Dan Bolser]

On Tue, 5 Oct 2004, Joe Landman wrote:

>For starters... use a good (P)RNG (rand is not appropriate for many real 
>research cases).  Have a look at Mersenne Twister 
>http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html and the Perl 
>module  http://search.cpan.org/~ams/Math-Random-MT-1.03/MT.pm .
>
>That said, you have to be careful about what random means in terms of 
>the specifics of the distribution.  If you are looking at CG rich 
>regions, you expect a good PRNG to give you effectively .25...  
>probability of any of the letters, so you will not get (unless you bias 
>the PRNG distribtion)  a CG rich set of "random" sequence data.
>
>Just some thoughts...

That reminds me, you can get random sequences 'in the syle of' a
particular HMM with HMMER (hmmemit). So you can build an hmm of a
particular family and then generate psudo family members, or use existing
hmm models for pfam / scop etc.



>
>Joe
>
>Dan Bolser wrote:
>
>>On Tue, 5 Oct 2004, Ryan Golhar wrote:
>>
>>  
>>
>>>Can anyone recommend a good random sequence generator program available
>>>for Linux?
>>>    
>>>
>>
>>perl -e '@x=qw(A T C G);for(1..10000){print $x[rand(@x)]}'
>>
>>Other than that it kind of depends on what your requirements are (and
>>aparently the above random generator isn't too good).
>>
>>perl -e '@x=qw(all work and no play);while(1){print $x[rand(@x)]}'
>>
>>
>>  
>>
>>>Ryan
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>>>
>>>    
>>>
>>
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>>  
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>
>