LGSFAligner:

• Source: LGSFAligner.zip ,  version 01 , author: Ngo Trung Hieu

• Usage: javac *.java  ;  java -mxABCm LGSFAligner score.txt input.txt (where ABC is the amount of memory)

• Input files: input.zip (input files should be in the same format as these examples)

LSSA:

• Source

• Modified source to compare the running time with our algorithm: lssa.zip

Related Software:

• RNAForester

Main Reference:

• Local Gapped Subforest Alignment and Its Applications in Finding RNA Structural Motifs

Other References:

• Local Sequence-Structure Motifs in RNA

• Local Similarity in RNA Secondary Structures

• Selenoprotein synthesis in archaea - identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion

• RNase P Database