NEBNext Custom RNA Depletion Design Tool

This tool designs probes to be used with the NEBNext RNA Depletion Core Reagent Set or to supplement an existing NEBNext Depletion Kit for the depletion of unwanted RNA species.

1. Target name

2. Email (for sending results)

3. Enter target RNA sequence

Please provide RNA (not cDNA) in FASTA format (5′→3′). See sample RNA input from NCBI.
Multiple sequences in FASTA format can be entered simultaneously.

4. Optional: cluster highly similar probes

This is suitable if your input RNA sequences are repetitive and/or if you would like to decrease the number of probes generated. We suggest somewhere between 0.6 and 0.8 as a reasonable range for redundant inputs. The default value of 0.7 indicates that probes with greater than 70% sequence identity will be clustered. See example.