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ChipCheck

Sequence Entry Page



Two sequences are given as an example in every textbox. Replace the entries with your own sequences entered in a similar fashion for your own calculations.

You will need to supply two sets of sequences in a FASTA-like format. The FASTA-Comment contains a nickname of the sequence, as well as the concentration (solution) or molar amount (on spot of chip), separated by a colon. The Comment line (starting with a ">" is followed by the sequence line that reports the actual sequence of the DNA strands.

Model entry for a concentration/amount of 1 picomolar/picomoles (entered as "1E-12" mol/l, where "E" means "to the power of 10"):

>nickname_of_sequence:1E-12
sequence

From this information, the thermodynamical data will be calculated using the program hybrid-min from the UNAFold software (by Drs. N. Markham and M. Zuker of Rensselaer Polytechnic Institute).

 

Sequences on chip : Sequences in solution :Help

Volume: l
Temperature: C
Salt concentration:
[Na+]   = mol/l
[Mg++]= mol/l

Type of duplexes formed: RNA-RNA DNA-DNA





Comments

Please note that the concentration of target strands and amount of probe strands, as well as the total volume of the solution from which the binding occurs is critical for the outcome.

To avoid misunderstandings: a volume of 3E-5 equals 30 microliters, 2E-4 equals 200 microliters, etc.

For problems bigger than 50X50 sequences (i.e. 2500 binding equilibria), using ChipCheck is not advisable, as the computational time will be too long. Please feel free to contact us to request access to ChipCheck (email: chipcheck"a"rrg.uka.de). The software UNAFOLD (by N. Markham and M. Zuker) needed by ChipCheck to generate the thermodynamic parameters can be accessed here. After installing both software packages, you will be able to generate input files locally on your computer.


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