In Silico Northern Blot

Pre-wet-lab small RNA analysis

Screen small RNA libraries using in silico northern blot

Upload small RNA libraries and a DNA probe to find candidates and inspect the result in a gel-like view.

Result availability: private result links and analysis data remain available for up to 90 days.

Run analysis Upload collapsed FASTA samples, enter a DNA probe, and set count and length filters. Check result Open a private result by UUID and explore thresholded matches, tables, and the illustrative blot. Open .isnb Inspect a saved result locally in your browser; the archive is never uploaded.

Supported workflow

A workflow to support your work

  1. Prepare each sample

    Each sample is normalized and filtered so RNA abundance can be compared.

  2. Find candidates

    BLAST finds candidate RNA, and a Hamming comparison checks how closely each candidate matches the probe.

  3. Visualize results

    Results are shown in a gel-like view so samples can be compared at a glance.

Result interpretation

Verified signal stays separate from ambiguity

Every verified RNA contributes its normalized abundance once; possible RNA stays visible separately.

Verified

A verified RNA contributes its normalized abundance once to the gel-like result.

Possible due to ambiguous bases

A possible match is reported separately because ambiguous bases may or may not match the probe, and it does not contribute signal.

Diagnostic

Possible RNA remains visible when ambiguity prevents a verified classification.