Grammar String is a novel representation of noncoding RNA secondary structure. By encoding both the sequence and secondary structure of ncRNAs in a string, ncRNA structural alignment is converted to sequence alignment. The software package provides an ncRNA consensus secondary structure derivation tool.
There are three sub-programs
1. ct2ss: The program to convert .ct file to secondary structure
2. ss2gs: The program to generate grammar string from sequence and structure
3. msa: The alignment program, pair-wise and multiple alignment program
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J Bioinform Comput Biol. 2011 Apr;9(2):317-37.
ncRNA consensus secondary structure derivation using grammar strings.
Achawanantakun R, Sun Y, Takyar SS.