DNA Melting - stitchprofiles.uio.no

Choose a type of calculationStitch profile Melting curve Probability profile Temperature profile Loop entropy

DNA sequence input

Upload a sequence file:

The sequence's GI number: in the NCBI GenBank. NCBI's Disclaimer and Copyright

Insert DNA sequence (copy/paste):

accggcagat tattatgggc cgccacgacg atgaacagac gctgctgcgt gtggatgagg
	 ccatcaataa aacctatacc cgccggaatg gtgcagaaat gtcgatatcc cgtatctgct
	 gggatactgg cgggattgac ccgaccattg tgtatgaacg ctcgaaaaaa catgggctgt
	 tccgggtgat ccccattaaa ggggcatccg tctacggaaa gccggtggcc agcatgccac
	 gtaagcgaaa caaaaacggg gtttacctta ccgaaatcgg tacggatacc gcgaaagagc
	 agatttataa ccgcttcaca ctgacgccgg aaggggatga accgcttccc ggtgccgttc
	 acttcccgaa taacccggat atttttgatc tgaccgaagc gcagcagctg actgctgaag
	 agcaggtcga aaaatgggtg gatggcagga aaaaaatact gtgggacagc aaaaagcgac
	 gcaatgaggc actcgactgc ttcgtttatg cgctggcggc gctgcgcatc agtatttccc
	 gctggcagct ggatctcagt gcgctgctgg cgagcctgca ggaagaggat ggtgcagcaa
	 ccaacaagaa aacactggca gattacgccc gtgccttatc cggagaggat gaatgacgcg
	  acaggaagaa cttgccgctg cccgtgcggc actgcatgac ctgatgacag gtaaacgggt
	  ggcaacagta cagaaagacg gacgaagggt ggagtttacg gccacttccg tgtctgacct
	  gaaaaaatat attgcagagc tggaagtgca gaccggcatg acacagcgac gcaggggacc
	  tgcaggattt tatgtatgaa aacgcccacc attcccaccc ttctggggcc ggacggcatg
  acatcgctgc gcgaatatgc cggttatcac ggcggtggca gcggatttgg agggcagttg
  cggtcgtgga acccaccgag tgaaagtgtg gatgcagccc tgttgcccaa ctttacccgt
  ggcaatgccc gcgcagacga tctggtacgc aataacggct atgccgccaa cgccatccag
  ctgcatcagg atcatatcgt cgggtctttt ttccggctca gtcatcgccc aagctggcgc

Extract DNA sequence fragment (optional):

Range: to Default [begin-end] to get the full sequence

Sequence length limitation: 240000bp, and it can be further reduced depending on amount of calculations.

Specify a temperature range for the melting curve:

How to handle the melting curve parameters

Temperature range (on the "x-axis"):
Interval from: °C to °C

This field will calculate a interval of temperatures and show a plot where the the DNA is melted at the calulated temperature

Helicity range (on the "y-axis"):
Interval from low: to high

This function will calculate helicity to the corresponding temperature.

Specify the stepsize in the interval in :

Relative steps:
OR
Manually: (advanced) °C
Ex.: Temperature interval [80, 85] with stepsize '1' will create a plot with the temperatures [80, 81, 82, 83, 84, 85]. See help for more examples.

Stepsize: The stepsize will determine the accuracy of the calculation. (Smaller resolution-Shorter calculatingtime & vs.)

Small -> 50% of Max stepsize
Medium -> 75% of max
High -> Max
Max stepsize is calculated out of maximum running time defined within the program.

Advanced options

What is this

Choose Loop Entropy Factor: Multiexponential approximation (fast) Exact power law (slow)

Choose empiric thermodynamic parameter set:

Salt concentration: [Na⁺] = M (Interval[0.001..8])

DNA Melting - Melting Curve