wseq :

sequences (contigs) at given window & overlap sizes chosen by the user

delG0 (37) :

Calculated by summing up individual dntd NN step-delG0(37) values from library of unified progression-energies.[get Source]

del G0(T) :

calculated using (delG0 = delH0 - T*delS0) at user-specified temperature (T), where 'delH0' and 'delS0' are predicted by summing up individual dntd NN step delH0 and delS0 values respectively from library of unified progression-energies. [get Source]

Tm (stacking-based, [Mon+]) (santalucia) :

Salt corrected by methods described in: J. Santalucia (Jr). Proc. Natl. Acid. Sci, USA 95, 1460-1465 (1998). Corrects only for monovalent counterions.

Tm (stacking-based, [Mon+] & [Mg+2]) (owczarzy) :

Salt corrected by methods described in: R.Owczarzy, B.G. Moreira, Y. You, M.A. Behlke, and J.A. Walder.Biochemistry 47, 5336–5353 (2008).Corrects for both monovalent & divalent (Mg+2) counterions.

Tm (%GC-based) (wetmur) :

Purely empirical %GC based length dependent Tm calculation (salt corrected intrinsically for monovalent counterions) adopted from methods described in: 1.J.G. Wetmur. Crit. Rev. BioChem. Mol. Bio. 26, 227-259 (1991).

NN :

Nearest Neighbour

dntd :


Notes to the users :

Users should remember that this is a purely in-vitro predictive model and is applicable only for contiguous strech of (genomic or plasmid) dsDNA
[Preferrably Polymeric (>16 bp)]

It does not treat these wseq(s) as physically fragmented piece of the quary-DNA, rather as a region of the contiguous thread being focussed by a vertual window at a time.

Users should beer in mind that biological DNA melting origins (Origins of replication, Transcription start sites etc) generally map to 'local minima of stability' with respect to their surroundings and more often than not are 'not the Global one'.

Users reporting results using the server should cite the follwoing refernce:

polDNAmelt: Local Melting Within Polymeric DNA—An Improved Method and Its Applications
Sankar Basu and Dhananjay Bhattacharyya*
Journal of Bioinformatics and Intelligent Control, 2013, 2 (4) : 316-320