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Scarna

Summary	Stem Candidate Aligner for RNA (Scarna) is a fast, convenient tool for structural alignment of a pair of RNA sequences. It aligns two RNA sequences and calculates the similarities of them, based on the estimated common secondary structures. It works even for pseudoknotted secondary structures.
Data type	RNA

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SCARNA Local Multiple

Summary	SCARNA_LM (SCARNA Local Multiple) is a local multiple aligner for RNA sequences. It is based on a discriminative pairwise alignment model which incorporates secondary structure features as base pairing probability calculrated by Rfold, and uses an efficient local multiple alignment construction procedure proposed by Phuong et al for local multiple alignment of protein sequences (cited from the original site).
Data type	RNA alignment

Summary

SCARNA_LM (SCARNA Local Multiple) is a local multiple aligner for RNA sequences. It is based on a discriminative pairwise alignment model which incorporates secondary structure features as base pairing probability calculrated by Rfold, and uses an efficient local multiple alignment construction procedure proposed by Phuong et al for local multiple alignment of protein sequences (cited from the original site).

Data type

RNA alignment

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seg-suite

Summary	The seg suite provides tools for manipulating segments and alignments. It uses a format called "seg". This program converts segments or alignments from various formats to seg.
Data type	DNA-sequence , RNA-sequence

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siExplorer

Summary	siExplorer is an algorithm developed for designing effective siRNAs on the basis of a statistical examination of RNAi activities and sequence characteristics.
Data type	RNA siRNA

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SlideSort

Summary	SlideSort is fast and exact method that can find all similar pairs from a string pool in terms of edit distance (cited from the original site).
Data type	DNA-sequence 　Protein-sequence

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SOKOS/CAN

Summary	SOKOS/CAN (pronounced So-ko-scan) is an experimental implementation of stochastic or probabilistic context-free grammar (SCFG) for RNA sequence analysis with capability of computing the marginalizes count kernel which is a metric similarity between two RNA sequences.
Data type	RNA , RNA sequence

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SPALN

Summary	Spaln is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.
Data type	Comparative genomics

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Stem Kernels

Summary	Stem Kernels is a kernel function for structural RNAs to measure a kind of similarity between a pair of RNA sequences from the viewpoint of secondary structures (cited from the original site).
Data type	RNA

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TACT

Summary	Transcriptome Auto-annotation Conducting Tool (TACT) is a web-based automated prediction tool of functional annotation that was developed by integrating ORF prediction, similarity search (BLASTX and FASTY) and motif prediction (InterProScan). TACT was produced in collaboration with the H-Invitational project, and has contributed to the development of the H-Invitational Database (H-InvDB).
Data type	DNA-sequence

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tantan

Summary	tantan is a tool to find cryptic repeats (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. You can get it from the archive page(cited from the original site).
Data type	DNA-sequence ,　RNA, Aminoacid

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