diffRNAbow

difference RNAbow

Attention:

Due to the computational burden of multiple partition function calculations, the maximum sequence length currently supported is 1700nt.
If Method=RNAstructure, only upper case letters can pair. Lower case letters are forced to be single-stranded, this has applications to chemical mapping experiments.

Example

If you copy and paste the Ferritin Light Chain sequence

001 GCAGTTCGGC GGTCCCGCGG GTCTGTCTCT TGCTTCAACA GTGTTTGGAC GGAACAGATC
061 CGGGGACTCT CTTCCAGCCT CCGACCGCCC TCCGATTTCC TCTCCGCTTG CAACCTCCGG
121 GACCATCTTC TCGGCCATCT CCTGCTTCTG GGACCTGCCA GCACCGTTTT TGTGGTTAGC
181 TCCTTCTTGC CAACCAACC

into the top sequence box, and the U22G mutant sequence

001 GCAGTTCGGC GGTCCCGCGG GGCTGTCTCT TGCTTCAACA GTGTTTGGAC GGAACAGATC
061 CGGGGACTCT CTTCCAGCCT CCGACCGCCC TCCGATTTCC TCTCCGCTTG CAACCTCCGG
121 GACCATCTTC TCGGCCATCT CCTGCTTCTG GGACCTGCCA GCACCGTTTT TGTGGTTAGC
181 TCCTTCTTGC CAACCAACC

into the bottom sequence box, with "wild type" for the top label and "U22G" for the bottom label, you will get a two-cluster RNAbow diagram.

Understanding the Output

The line thickness of each arc is proportional to the probability of forming a base pair between the two bases.
Red arcs denote base pairs which are unique to the top cluster.
Blue arcs denote base pairs which are unique to the bottom cluster.
Black arcs are base pairs common to both clusters.

Input mode
Top Sequence (plain, FASTA, GenBank, etc.) [?]
Bottom Sequence (plain, FASTA, GenBank, etc.) [?]
Top Label
Bottom Label
Method