RNA Secondary Structure

IGV can be used to visualize RNA secondary structures in arcs connecting base pairs (the linear format). Alternative structures, where one nucleotide is involved in more than one base pair, and pseudo knots, where arcs cross, can be accommodated.

To visualize the structures, the base pairing information should be stored in a bed format file, which is quite similar to the commonly used 'connect format’ described by the mfold program (Zuker 2003, PMID: 12824337). The file must include a track line which species graphType=arc, e.g. "track graphType=arc”. Each record line must contain the first three columns of a bed file: chrom, start and end, where the start and end represent the base pair. Note that the start position follows standard BED file convention and is zero-based (first base on a sequence is position 0). The following small example represent a hypothetical stem loop:

track graphType=arc
chr1 10 25 stemloop1
chr1 11 24 stemloop1
chr1 12 23 stemloop1
chr1 13 22 stemloop1
chr1 14 21 stemloop1
chr1 15 20 stemloop1

Additional examples can be found in the supplement of the following paper Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016 May 12.