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<font face="sans-serif">Hi Bhakti,<br>
<br>
My old code for calculating degenerate PCR primer Tm has been lurking
unloved on my computer for a while, so I've uploaded some snippets to
the BioPerl wiki scrapbook at
<a class="moz-txt-link-freetext"
href="http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook">http://www.bioperl.org/wiki/Category:PCR_Primers/Scrapbook</a>.<br>
<br>
The code uses BioPerl together with Primer 3. I don't have a pure perl
implementation. </font><font face="sans-serif">I can't remember what </font><font
face="sans-serif">Tm calculation </font><font face="sans-serif">methods
are
available through Primer 3, but I believe there are several methods
in the documentation. I haven't seen a method for calculating the Tm of
primers with Inosine, but that may not matter to you.<br>
<br>
</font><font face="sans-serif">The constituents of degenerate primers
can have a wide range of melting temperatures, so finding forward and
reverse primers that operate within an acceptable range could be
tricky. As for what constitutes an acceptable temperature range, I
suggest you consult your nearest friendly PCR technician. If you get
any sensible answers please report back.<br>
</font><font face="sans-serif"><br>
I hope this helps, please let me know how you get on.<br>
<br>
Giles<br>
</font><br>
On 14/04/10 18:20, Bhakti Dwivedi wrote:
<blockquote
cite="mid:n2jb643abd21004141020m828a06d0xbe84cc06b2cc1731@mail.gmail.com"
type="cite">
<pre wrap="">Does anyone know how to compute the melting temperature for Degenerate
Primers following the thermodynamic nearest neighbor model? or how it
works? what I found so far is Tm calculations for primers with A,C,G, or T
only, but haven't came across anything that can help me explain the way it
works for degenerate primers, so I can implement that in my perl code.
any help please? Thanks!
Bhakti
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