ProbeMelt - Inputs

FISH

• The ProbeMelt tool for FISH probes is described in:

  ES Wright et al. (2014) "Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for Accurate Identification." Applied and Environmental Microbiology, doi:10.1128/AEM.01685-14.

• Enter one or more pairs of probe (DNA) and target (RNA) sequences separated by new lines, and select their orientation from the drop down menu. Alternatively, enter probe and/or target sequences in FASTA format. If only a single probe or target is provided then this sequence is recycled so that the number of probes and targets is equal.
• The letters 'A', 'C', 'G', 'T', and '-' are recognized as their corresponding nucleotides or gap. The letters 'T' and 'U' in the target sequence(s) are both treated as 'U'.
• Ambiguity codes (i.e., 'N') in the probe and target sequences are permitted when they will result in perfect match pairs. Ambiguous probe sequences without a corresponding perfect match target permutation are not permitted.
• By default the program will align each probe to its target sequence in order to find the target site. Aligned probe/target sequences of equal length can also be used if 'Aligned' is selected.
• Up to 1MB of probe/target sequences can be processed in a single run. This corresponds to about 1,000 probes of length 20 with targets of length 1,500 nucleotides. Entries greater than 1MB will result in an error.

Microarray

• The ProbeMelt tool for microarray probes is described in:

  LS Yilmaz et al. (2012) "Modeling Formamide Denaturation of Probe-Target Hybrids for Improved Microarray Probe Design in Microbial Diagnostics." PLoS ONE, doi:10.1371/journal.pone.0043862.

• Enter one or more pairs of DNA sequences separated by new lines and select the correct orientation from the drop down menu. The letters 'A', 'C', 'G', 'T', and '-' are recognized as their corresponding nucleotides or gap. Other characters, such as degeneracy codes (e.g., 'N'), will result in an error being shown.
• By default the program will align each probe to each target in order to find its target site. If 'Unaligned' is selected then any gaps in the probe or target will be removed before alignment. If 'Aligned' is selected then each pair of probe and target sequences must be the same length.
• Up to 1MB of probe/target sequences can be processed in a single run. This corresponds to about 19,000 probe and target pairs of length 25 nucleotides. Entries greater than 1MB will result in an error.