[BiO BB] Random Sequence Generator

Fei Li bioinformatics2005 at yahoo.com.cn
Wed Oct 6 08:18:47 EDT 2004

I do not think we can find a general random sequence generator for all the case.  At least, we need consider GC content, and maybe even content of  "GC", "GG", "GT", "GA"......"TC"....."TA", etc.   A "real" random sequnce is most likely useless in a specific case. 

Dan Bolser <dmb at mrc-dunn.cam.ac.uk> wrote:

On Tue, 5 Oct 2004, Joe Landman wrote:

>That said, you have to be careful about what random means

>Just some thoughts...

That reminds me, you can get random sequences 'in the syle of' a
particular HMM with HMMER (hmmemit). 

>Dan Bolser wrote:
>>On Tue, 5 Oct 2004, Ryan Golhar wrote:
>>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)]}'

Fei Li, PhD, Postdoc fellow
Institute of Bioinformatics
MOE key laboratory of Bioinformatics
Tsinghua University
Beijing, 100084
E-mail: flee at tsinghua.edu.cn

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