SLICSel 1.1

About the program:

SLICSel is a program for designing specific oligonucleotide probes for microbial detection and identification. To obtain maximal specificity of designed oligonucleotides, SLICSel uses the Nearest-Neighbor thermodynamics-based approach for probe design.

Here is a sample target file and sample non-target file.

For further information please contact: and please check the HELP page.

There have been 999 submissions to this web site since June 2007.

Please insert your target sequence(s) in FASTA format:
or upload your target sequence file:
Please insert your non-target sequence(s) in FASTA format:
or upload your non-target sequence file:
Please select ESSENTIAL parameters for your oligonucleotide probes:

Probe melting temperature interval (min - max): - (°C)

Annealing temperature for calculations will be: (°C)

Minimal binding energy (ΔG) difference between target and non-target sequences: (-kcal/mol)

Maximal binding energy (ΔG) difference between target sequences: (-kcal/mol)

Use thermodynamics
Additionally, you can adjust OPTIONAL parameters for your oligonucleotide probes:

Probe length, default: (nucleotides)

Number of mismatches required with non-target sequences, default: (nucleotides)

Concentration of monovalent cations ([Na]), default: (mM)

Concentration of nucleic acids ([target molecules]), default: (nM)

Check the formation of probe secondary structures (mfold)?

Please select additional genome(s) against which you need to test the uniqueness of your probes (optional, slightly extends the design time):
Bacteria (click to open, click again to clear)
Eukaryota (click to open, click again to clear)
If you enter your email address, you will get an email when SLICSel is finished (optional):

University of Tartu, Department of Bioinformatics 2017