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A Method for Extracting Optimal Sequence Related to Biological Activity

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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 typeDNA-motif
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CentroidAlifold

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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 typeRNA secondary structure
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CentroidAlign

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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 typeRNA alignment
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CentroidFold

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SummaryCentroidFold is a software to predict RNA second structure and common second structure. A benchmark test shows it performs better than Mfold and RNAfold.
Data typeRNA
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CentroidHomfold

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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 typesecondary structure
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ChIP2LAMP

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SummaryDiscovery 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

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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 typeRNA
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Dnemulator

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

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SummaryFdur computes sufficient statistics of phylogenetic tree model(cited from original site).
Data typeRNA
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HEAT

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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 typeAnnotation
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IPknot

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SummaryRNA pseudoknot prediction based on maximizing expected accuracy (cited from the original site).
Data typeRNA pseudoknot
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Idiographica

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SummaryIdiographica 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 typeChromosome
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LAMPLINK

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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 typeDNA-sequnece
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LAST

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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

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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 typeDNA-sequence alignment
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MXSCARNA

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SummaryMXSCARNA (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 typeRNA (RNA sequence)
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Murlet

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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 typeRNA
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PHMMTS

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SummaryPHMMTS (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 typeRNA
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PMID-Extractor

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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 typeJournal
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PSTAG

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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 typeRNA
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RNAmine

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SummaryRNAmine is software for extracting stem patterns that frequently appear from RNA sequences using a graph mining.
Data typeRNA
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Raccess

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SummaryRaccess is the tool for genome-scale computation of structural accessibility of RNA transcripts (cited from the original site).
Data typeRNA
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RactIP

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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 typeRNA RNA-RNA interaction
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Rchange

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SummaryRchange compute energy changes of RNA secondary structures in response to base mutations(cited from original site).
Data typeRNA
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Recount

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SummaryRECOUNT 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 typeDNA-sequence  Next Generation Sequencing Data
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Rentropy

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

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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 typeRNA
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SAMURAI

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SummaryGene 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 typeGene expression
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SCARNA Local Multiple

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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 typeRNA alignment
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SOKOS/CAN

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SummarySOKOS/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

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SummarySpaln 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 typeComparative genomics
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Scarna

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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 typeRNA
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SlideSort

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SummarySlideSort 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 typeDNA-sequence  Protein-sequence
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Stem Kernels

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SummaryStem 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 typeRNA
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TACT

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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 typeDNA-sequence
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Web page checker

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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 typeWeb contents
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miRRim

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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 typeRNA  (miRNA)
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paraclu

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SummaryParaclu finds clusters in data attached to sequences(cited from original site).
Data typeDNA-sequence
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seg-suite

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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

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SummarysiExplorer is an algorithm developed for designing effective siRNAs on the basis of a statistical examination of RNAi activities and sequence characteristics.
Data typeRNA siRNA
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tantan

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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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