dna.bio.keio.ac.jp

bpla-kernel.dna.bio.keio.ac.jp

index.html

BPLA kernels for structural RNA analysis. URL:bpla kernel-1.1.tar.gz. URL:bpla kernel-1.0.tar.gz. Supplementary materials for [Morita et al., Nucleic Acids Res, 2009]. These files contain the annotations data for WormBase. The candidates analyzed by qRT-PCR URL:http:/ bpla-kernel.dna.bio.keio.ac.jp/ce-candidates.wig. The candidates whose class probability is 0.9 URL:http:/ bpla-kernel.dna.bio.keio.ac.jp/ce-p0.9.wig. The candidates whose class probability is 0.9 and overlapped with mapped ESTs URL:htt...

phmmts.dna.bio.keio.ac.jp

PHMMTS - Home

This page provides an implementation of the pair hidden Markov models on tree structures (PHMMTSs). Which is an extension of the. Pair hidden Markov models (PHMMs. Defined on alignments of trees. PHMMTS provides a unifying framework and an automata-theoretic model for alignments of trees, structural alignments and pair stochastic context-free grammars. By structural alignment, we mean a pairwise alignment to align an unfolded RNA sequence into an RNA sequence of known secondary structure.

osfinder.dna.bio.keio.ac.jp

OSfinder - Home

OSfinder: A Tool for Accurate Orthology Mapping. Public release of OSfinder v1.4. Modify Perl scripts for drawing synteny maps. Public release of OSfinder v1.3. Modify merge algorithm so as to compute orthologous segment robustly. Public release of OSfinder v1.2. Add Perl scripts for automatically downloading genome sequence files from the NCBI GenBank database or protein sequence files from the Ensembl genome browser. Public release of OSfinder v1.1. Public release of OSfinder v1.0.

murasaki.dna.bio.keio.ac.jp

Murasaki Project: Murasaki Project - Murasaki Project

New version released (Jun.28, 2012). Murasaki is published in PLoS ONE. An addon tool for Murasaki to compare translated genome sequence. (Sep.11, 2009). For the latest changes see the changelog. Quick Download †. Latest Mac binary builds are available here: http:/ lut.eee.u-ryukyu.ac.jp/project.html.en. If you're new to Murasaki, please check the installation procedures in Murasaki. Aug24, 2010 23:18:18 JST. Jun28, 2012 13:29:53 JST. Jun28, 2012 13:29:52 JST. Recent Wiki updates †. PukiWiki 1.4.7.

metavelvet.dna.bio.keio.ac.jp

Metagenomic Assembler

An extension of Velvet assembler to de novo metagenomic assembly. MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads. MetaVelvet - SL : An extension of Velvet assembler to de novo metagenomic assembler utilizing supervised learning. Namiki T*, Hachiya T*, Tanaka H, Sakakibara Y. (2012) MetaVelvet : An extension of Velvet assembler to de novo. Metagenome assembly from short sequence reads. 40(20), e155. ( Summplementary figures and tables.

rtips.dna.bio.keio.ac.jp

Rtips

Ructure prediction using IP. Web server provides services for predicting RNA complicated secondary structures of given sequences, including intramolecular pseudoknots and joint structures formed from two RNAs. The programs in Rtips run fast and predict the maximum expected accuracy (MEA) structure using integer programming (IP). Let's get started by moving to respective services IPknot. RNA secondary structure prediction including pseudoknots. RNA-RNA interaction (joint secondary structure) prediction.

pstag.dna.bio.keio.ac.jp

PSTAG - Home

This software provides an implementation of the pair stochastic tree adjoining grammars (PSTAGs). For modeling 'pseudoknot' RNA structures, which is an extension of the pair hidden Markov models on tree structures (PHMMTSs). PSTAG is a novel method for structural alignment to align and predict RNA secondary structures including pseudoknots. By structural alignment, we mean a pairwise alignment to align "an unfolded RNA sequence" into "an RNA sequence of known secondary structure". Revised Sep 21, 2004.

xgenovo.dna.bio.keio.ac.jp

An Extended Genovo

An Extended Genovo Metagenomic Assembler by Incorporating Paired-End Information. An Extended Genovo Metagenomic Assembler by Incorporating Paired-End Information. Cite "An Extended Genovo" as :. Afiahayati, Sato K, Sakakibara Y. (2013) An extended genovo metagenomic assembler by incorporating paired-end information. PeerJ 1:e196 http:/ dx.doi.org/10.7717/peerj.196. Published works of the past 12 months related to this research. Bioinformatics 2012, 28(11):1455 1462. Bioinformatics 2012, 28(11):1420 1428.