SCARNA:Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-length Stem Fragments

Yasuo Tabei, Koji Tsuda, Taishin Kin and Kiyoshi Asai

Supplementary information

Dataset1

Dataset for calculating the Fig.2, Fig.3 and Fig.4 of supplementary material. Refernce alignment files are for calculating the SPS and the SCI of reference.
sps_file.tar.gz and sci_file.tar.gz are the SPS and SCI calculated by SCARNA, ClustalW Foldalign2.0.

family name(Rfam number)	fasta files	reference alignment files	SCARNA,ClustalW and Foldalign2.0 SPS file	SCARNA, ClsutalW and Foldalign2.0 SCI file	SPS jpg	SCI jpg
5S ribosomal RNA(RF00001)	fasta_files.tar.gz	reference_alignment_files.tar.gz	sps_file.csv	sci_file.csv	SPS jpg	SCI jpg
5.8S ribosomal RNA(RF00002)	fasta_files.tar.gz	reference_alignment_files.tar.gz	sps_file.csv	sci_file.csv	SPS jpg	SCI jpg
Hammerhead ribozyme(RF00008)	fasta_files.tar.gz	reference_alignment_files.tar.gz	sps_file.csv	sci_file.csv	SPS jpg	SCI jpg

Dataset2

Dataset for calculating Fig.11. Reference Structure CTs are CT files of reference secondary structure.
Result of SCARNA and CARNAC prediction are calculated from the datasets.

Percentage of Stems	Fasta Files	Reference Structure CTs	Result of SCARNA Prediction	Result of CARNAC Prediction	jpg
25-50%	25-50_fasta.zip	reference_25-50.zip	SCARNA_25-50.txt	CARNAC_25-50.txt	25-50 jpg
50-75%	50-75_fasta.zip	reference_50-75.zip	SCARNA_50-75.txt	CARNAC_50-75.txt	50-75 jpg