iFISH Probe Designer

Here you can design new single probes or spotting probes. Go to the Single Probe tab to design one probe in a region of interest. Instead, to query for a number of probes in a single region of interest use Spotting Probe. In the Databases tab you can scroll through the available databases. To go to a previously ran query, use the search tool. You can also check how many queries are currently in the Queue. More details in the help page.

General

Where

What

2 The more probe candidates you output, the longer the query will take.

Advanced settings

Feature Use Size
(minimize)
Centrality
(maximize)
Homogeneity
(maximize)
First1 Filter probe candidates.
Second Rank probe andidates.
Third Not used.

1 Candidate probes are selected based on the first feature, in the range best_f1_value±(best_f1_value · threshold).

General

Where

What

Advanced settings

Feature Use Size
(minimize)
Centrality
(maximize)
Homogeneity
(maximize)
First1 Filter probe candidates.
Second Rank probe candidates.
Third Note used.

1 Candidate probes are selected based on the first feature, in the range best_f1_value±(best_f1_value · threshold).

  • Available databases:
  • iFISH-40mer
    if_kmer40_dtm10_gcmin35_gcmax80_hpolyes_db
    • Reference genome: hg19
    • Minimum oligo distance: 10 nt
    • Oligo length range: 40-40 nt
    • Overlapping oligos: False
    • deltatm: 10 degC
    • gcrange: 35-80
    • homopolymers: 7+
    • software: iFISH
    • authors: Gelali E, et al.

    Reference: Gelali E, et al., "iFISH is a free resource enabling versatile DNA FISH to study genome architecture in single cells." In revision.

    Database link
    • Reference genome: hg19
    • Minimum oligo distance: 0 nt
    • Oligo length range: 35-41 nt
    • Overlapping oligos: False
    • software: OligoMiner
    • parameters: balanced
    • authors: Beliveau BJ, et al.

    Reference: Beliveau, Brian J., et al. "OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes." Proceedings of the National Academy of Sciences (2018): 201714530.

    Database link
    • Reference genome: hg19
    • Minimum oligo distance: 0 nt
    • Oligo length range: 26-32 nt
    • Overlapping oligos: False
    • software: OligoMiner
    • parameters: coverage
    • authors: Beliveau BJ, et al.

    Reference: Beliveau, Brian J., et al. "OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes." Proceedings of the National Academy of Sciences (2018): 201714530.

    Database link
    • Reference genome: hg19
    • Minimum oligo distance: 0 nt
    • Oligo length range: 40-46 nt
    • Overlapping oligos: False
    • software: OligoMiner
    • parameters: stringent
    • authors: Beliveau BJ, et al.

    Reference: Beliveau, Brian J., et al. "OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes." Proceedings of the National Academy of Sciences (2018): 201714530.

    Database link