#29 · Tools & infrastructure
Browser servers now address RNA structure, primer design, H-DNA and genomic analysis
The common thread is packaging established sequence and structure analyses as free, browser-accessible tools. ShapeRNA and RNAanalyzer3 are free web servers covering RNA secondary structure, SHAPE/DMS-guided modeling, ensemble inference, and motif discovery, with RNAanalyzer3 linking motif hits to Rfam and miRBase. PrimerWeaver offers browser-based primer design for overlap PCR, mutagenesis, multiplex PCR, and Gibson, Golden Gate, and USER cloning, computed locally. GEAR bundles Sanger chromatogram viewing, alignment, and primer and probe design in an open-source platform. HSeeker, a Python tool with a web app, identifies and scores H-DNA-forming mirror repeats using a center-outward search and overlap removal. The summaries describe integration and accessibility rather than novel algorithms, and they report no quantitative benchmarks.
Published papers
ShapeRNA: an integrated web server for RNA secondary structure, ensemble, and functional analysis.
ShapeRNA is a free web server integrating RNA secondary structure prediction, SHAPE/DMS-guided modeling, ensemble inference, and structure-aware regulatory…
RNA motifs, RNA structure, and motif context analyzed by RNAanalyzer3.
RNAanalyzer3 is a free web server for RNA motif discovery, structure prediction, and motif-in-context analysis, linking hits to Rfam and miRBase with batch…
PrimerWeaver: an integrated web server for primer design in molecular biology workflows.
Free browser-based primer design tool covering overlap PCR, mutagenesis, multiplex PCR, and Gibson/Golden Gate/USER cloning, computed locally.
GEAR Genomics: a user-friendly, open-source web platform enabling interactive genomic analysis for molecular biologists.
GEAR is an open-source, browser-based genomics web platform bundling interactive tools for Sanger chromatogram viewing, alignment, primer and probe design,…
Preprints
HSeeker: an algorithm for systematic H-DNA sequence identification
HSeeker is a Python tool and web app that identifies and scores H-DNA-forming mirror repeats using a center-outward search, overlap removal, and thermodynamic…
Topic history
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