[Bioperl-l] bioperl modules

Chris Fields cjfields at illinois.edu
Fri Jul 23 09:17:41 EDT 2010

This sounds suspiciously like homework, so I'm reluctant to give any direct answers.  Most (all?) of these are covered in the Tisdall books, IIRC, and all use regexes or transliteration, that's about all I'll say.


On Jul 23, 2010, at 6:31 AM, Giles Weaver wrote:

> 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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