Nucleic Acid Support

Colour Schemes

Jalview has color schemes for nucleic acid based sequences, ability to fetch sequences from RFAM and RNA secondary structure coloring

Information on the Nucleotide colour scheme and Purine/Pyrimidine colour scheme are available under the Colour Menu. See Colour Schemes.

RNA Support

Sequences can be fetched from the RFAM database by accession number or ID.

If an RNA alignment is loaded from a Stockholm file with secondary structure information in WUSS notation, the alignment can be coloured by the helices in the secondary structure. Helices are determined by the base-pairing in the secondary structure line. See RNA Helices Colouring. Below is an example of this type of coloring

Annotation panel shows the presence of RNA helices and WUSS notation from input file specifying secondary structure.