[Bioperl-l] bioperl modules

Giles Weaver giles.weaver at bbsrc.ac.uk
Fri Jul 23 07:31:11 EDT 2010


See http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook for Tm 
calculation.
Most of the other checks are trivially easy in perl/bioperl, with the 
exception of checks for hairpin and dimer formation - I'd be interested 
to hear if anyone has implemented these checks.

Regards,

Giles

On 23/07/10 12:01, Shachi Gahoi wrote:
> I want to use following bioperl modules. I have installed bioperl 1.6.I.
> have searched all modules in it but i have not found following modules. I
> want to use it. please tell me if anyone know about these modules and use of
> it.
>
> temp- for temperature checking
> ac- for count of AC content
> gc- for count of GC content
> dimer- check bases for dimerization
> check 5- Check the presence of GC, CG, C or G at 5'
> check 3- Check the presence of GC, CG, C or G at 3'
> basepair- calculate % of GC
> hairpin- calculate hairpin structure
> delta- calculate delta G value for primer
> temp diff- check for temperature difference in left and right primer
>
> please tell me if anyone know about these modules.
>
> Thanks in advance
>
>
>    


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