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A Method for Extracting Optimal Sequence Related to Biological Activity

Summary	This software can extract the optimal sequence relating to biological activity, if we have the data composed of sequences and corresponding activity, regardless of definition of characteristic sequence (cited from the original site).
Data type	DNA-motif

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CentroidAlifold

Summary	CentroidAlifold provides Accurate (common) secondary structure prediction for aligned RNA sequences.You can download CentroidAlifold software , which was contained in CentroidFold package (cited from the original site).
Data type	RNA secondary structure

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CentroidAlign

Summary	An accurate and fast aligner for multiple RNA sequences, based on maximizing the expected sum-of-pair score (SPS).　You can get the archive file for linux and windows (cited from the original site).
Data type	RNA alignment

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CentroidFold

Summary	CentroidFold is a software to predict RNA second structure and common second structure. A benchmark test shows it performs better than Mfold and RNAfold.
Data type	RNA

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CentroidHomfold

Summary	CentroidHomfold provides RNA Secondary Structure prediction using Homologous Sequences.You can download CentroidHomfold software, which was contained in CentroidFold, or use CentroidHomfold-LAST Web-Server (cited from the original site).
Data type	secondary structure

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ChIP2LAMP

Summary	Discovery of combinatorial regulations is a key to understand complex gene regulation machineries. Combining this scripts (chip2lamp) with a statistical analysis LAMP allows us to find statistically significant combinations by integrating ChIP-seqs and RNA-seqs. This can handle MACS1/2 result as a ChIP-seq peak caller and Cuffdiff result from RNA-seq.
Data type	ChIP-sequence, RNA-sequence

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DAFS

Summary	Simultaneous aligning and folding of RNA sequences by dual decomposition. DAFS can take FASTA formatted RNA sequences as input, then producea structural alignment.
Data type	RNA

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Dnemulator

Summary	DNemulator is a package for simulating DNA sequencing errors, polymorphisms, cytosine methylation and bisulfite conversion.
Data type	DNA-sequence

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Fdur

Summary	Fdur computes sufficient statistics of phylogenetic tree model(cited from original site).
Data type	RNA

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HEAT

Summary	H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. This technique is called Gene Set Enrichment Analysis (GSEA), and is popularly used in analyzing results of microarray experiments. Fisher's exact probability is used in statistical tests of HEAT.
Data type	Annotation

Summary

H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. This technique is called Gene Set Enrichment Analysis (GSEA), and is popularly used in analyzing results of microarray experiments. Fisher's exact probability is used in statistical tests of HEAT.

Data type

Annotation

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Idiographica

Summary	Idiographica is a web server for you to create your own idiogram. Please fill the following web form and click on the submit button. The Idiographica server will send you an email to notify the completion of the idiogram creation task. You can use the generated idiograms without any restriction or obligation.(cited from the original site)
Data type	Chromosome

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IPknot

Summary	RNA pseudoknot prediction based on maximizing expected accuracy (cited from the original site).
Data type	RNA pseudoknot

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LAMPLINK

Summary	The LAMPLINK can detect statistically significant epistatic interactions of two or more SNPs from GWAS data. This software can be used in the same way as the widely used GWAS analysis software PLINK, but LAMPLINK has the additional options for the detection of epistatic interactions with LAMP, which is a multiple testing procedure for combinatorial effects discovery.
Data type	DNA-sequnece

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LAST

Summary	LAST is a software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very large amounts of sequence data. It can also report probabilities for every pair of aligned letters, indicating the reliability of each pairing.
Data type	DNA-sequence ,RNA, protein, user-defined alphabet.

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MAFFT

Summary	MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of
Data type	DNA-sequence alignment

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miRRim

Summary	miRRim is a method for detecting miRNA foldbacks based on hidden Markov model (HMM). In this method, the evolutionary and secondary structural features of a miRNA region is represented by a sequence of multidimensional vectors. HMMs that generate a sequence of continuous values are used to model the feature vector sequences.(cited from the original site)
Data type	RNA 　(miRNA)

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Murlet

Summary	Murlet is a multiple alignment tool for RNA sequences using iterative alignment based on Sankoff's algorithm with sharply reduced computational time and memory. This was developed by Computational Biology Research Center (CBRC), AIST.
Data type	RNA

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MXSCARNA

Summary	MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA.
Data type	RNA (RNA sequence)

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paraclu

Summary	Paraclu finds clusters in data attached to sequences(cited from original site).
Data type	DNA-sequence

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PHMMTS

Summary	PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure (cited from the original site).
Data type	RNA

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PMID-Extractor

Summary	PMID-Extractor allows a user to obtain PubMed IDs (PMIDs) from PDF files or text format files of journal paper in your hand. From Digital Object Identifiers (DOIs, http://en.wikipedia.org/wiki/Digital_object_identifier) or text information (e.g. titles) in the first page of each files, To start using PubMedScan, a paper recommender, PMIDs are required to specify the users' interest. That is the main usage of PMID-Extractor.
Data type	Journal

Summary

PMID-Extractor allows a user to obtain PubMed IDs (PMIDs) from PDF files or text format files of journal paper in your hand. From Digital Object Identifiers (DOIs, http://en.wikipedia.org/wiki/Digital_object_identifier) or text information (e.g. titles) in the first page of each files, To start using PubMedScan, a paper recommender, PMIDs are required to specify the users' interest. That is the main usage of PMID-Extractor.

Data type

Journal

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PSTAG

Summary	PSTAG (Pair Stochastic Tree Adjoining Grammars) is for RNA sequences including pseudoknotted structures.The program based on PSTAGs is the first grammar-based and practically executable software for comparative analyses of RNA pseudoknot structures, and, further, non-coding RNAs (cited from the original site).
Data type	RNA

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Raccess

Summary	Raccess is the tool for genome-scale computation of structural accessibility of RNA transcripts (cited from the original site).
Data type	RNA

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RactIP

Summary	RactIP can provide fast and accurate prediction of RNA-RNA interaction using integer programming. 4 tool archives (Source(version0.0.1 and 0.0.2), Windows, Linux) are ready.
Data type	RNA RNA-RNA interaction

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Rchange

Summary	Rchange compute energy changes of RNA secondary structures in response to base mutations(cited from original site).
Data type	RNA

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Recount

Summary	RECOUNT is a software for estimating the true count of Solexa readsbased on a probabilistic model. RECOUNT uses the quality score provided by Solexa and the reads as its input. Typical application of this software is for transcriptome or metagenomic expression analysis (cited from the original site).
Data type	DNA-sequence 　Next Generation Sequencing Data

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Rentropy

Summary	Rentropy computes entropy, mean energy, and variation of energy from the Boltzmann distribution of RNA secondary structures(cited from original site).
Data type	RNA

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Rfold

Summary	A base pair probability matrix that indicates the ease of secondary base energy pairing has often been used for sequence analysis of structural RNA. In recent years, it has been found that large amounts of non-protein-encoding RNAs are transcribed in higher eukaryotes, and in order to conduct sequence analysis of these RNAs, There is an increasing need for methods of determining local base pair probabilities where the distance is limited to W or less. In the past, there were only programs that used such probability calculations to use unrealistically simplified models and those that used approximate calculation methods. Rfold is the first software that can calculate local base pair probabilities without approximation based on the energy model of secondary structure. When the sequence length is N, Rfold calculates local base pair probability with the time complexity of O (NW2) and the complexity of O (N + W2) region. Furthermore, Rfold is implemented with an algorithm that predicts secondary structures based on the Maximal Expected Accuracy method, which has recently been validated.
Data type	RNA

Summary

A base pair probability matrix that indicates the ease of secondary base energy pairing has often been used for sequence analysis of structural RNA. In recent years, it has been found that large amounts of non-protein-encoding RNAs are transcribed in higher eukaryotes, and in order to conduct sequence analysis of these RNAs, There is an increasing need for methods of determining local base pair probabilities where the distance is limited to W or less. In the past, there were only programs that used such probability calculations to use unrealistically simplified models and those that used approximate calculation methods. Rfold is the first software that can calculate local base pair probabilities without approximation based on the energy model of secondary structure. When the sequence length is N, Rfold calculates local base pair probability with the time complexity of O (NW2) and the complexity of O (N + W2) region. Furthermore, Rfold is implemented with an algorithm that predicts secondary structures based on the Maximal Expected Accuracy method, which has recently been validated.

Data type

RNA

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RNAmine

Summary	RNAmine is software for extracting stem patterns that frequently appear from RNA sequences using a graph mining.
Data type	RNA

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SAMURAI

Summary	Gene expression networks have different gene components depending on the cell types. SAMURAI is a tool for finding such minimal functional units of genes called modules from large-scale gene expression data. Modules are searched against by an ultra fast and exhaustive biclustering method using a closed itemset mining algorithm.suspending for relocation. (confirmation on 2012/11/05)
Data type	Gene expression

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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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Web page checker

Summary	A web page checker. This tool can monitor web pages, and grouping of web pages, highlight changes in a page, and send Email reports.
Data type	Web contents

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