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CorreLogo Homepage

3D sequence logos of RNA and DNA alignments

The CorreLogo server generates for a given RNA or DNA sequence alignment a three-dimensional representation in VRML format and JavaView JVX format. The generated model contains quantities like mutual information, composition and single column information ("conservation") in one three-dimensional representation. This can be useful for visual inspection of the properties of a nucleotide sequence alignment and for RNA secondary structure prediction.

This web server was developed in the research group of Dr. Bruce Shapiro in collaboration with Dr. Tom Schneider.

This server is hosted by the Advanced Biomedical Computing Center (ABCC) of the National Cancer Institute (Frederick Campus).

Important links:

CorreLogo Submission Form: Submit RNA and DNA alignments to generate 3D logos.

CorreLogoRetrieve: Retrieve old CorreLogo result files with the file retriever.

CorreLogo help page: Obtain more information about how to use the CorreLogo server.

KNetFold web server page: RNA consensus secondary structure prediction with KNetFold.

RnaJunction database: A database of RNA junctions and kissing loops.


Small example (tRNA anticodon)
Loop E region
Large example (tRNA)


E. Bindewald, T.D. Schneider, B.A. Shapiro:

CorreLogo: An online server for 3D sequence logos of RNA and DNA alignments

Nucleic Acids Res. 2006 Jul 1;34 (Web Server issue):W405-11.