MEDALS METI Life science integrated database portal site

ALN

Summary	Aln is a program for aligning a pair of nucleotide or amino acid sequences or alignments. Aln can even align a nucleotide sequence and a single or a group of protein sequences. This can be used to predict eukaryotic gene structures (protein-coding exons) based on sequence homology with known protein sequences.
Data type	DNA, amino acid sequences

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ALNGG

Summary	ALNGG detects the protein coding gene by genome comparison between two species.
Data type	DNA-sequence , Genome

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ASIAN

Summary	ASIAN is a tool for automatically inferring the relationships between objects from data including redundant information, e.g. expression profiles that were measured for a large number of genes under various conditions.The tool combines cluster analysis, regression analysis, and graphical Gaussian modeling.By inputting your raw data, you can obtain some relationships between objects: the correlation, the grouping, the group number, and the network graph.
Data type	Gene expression profile

Summary

ASIAN is a tool for automatically inferring the relationships between objects from data including redundant information, e.g. expression profiles that were measured for a large number of genes under various conditions.The tool combines cluster analysis, regression analysis, and graphical Gaussian modeling.By inputting your raw data, you can obtain some relationships between objects: the correlation, the grouping, the group number, and the network graph.

Data type

Gene expression profile

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CoCoozo

Summary	CoCoozo is a search engine for analyzing MS spectrum data. CoCoozo performs parallelized high-speed database search with a set of MS spectrum data against existing protein sequence databases in order to identify proteins corresponding to the precursor ions from peak intensity patterns.
Data type	Ptotein-sequence

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Data mining analysis of supersecondary structure

Summary	The DCCP method (Dictionary of Conformational Code in Proteins) converts 3D information of protein X-ray crystal structure data to 1D information, and converts. Its conformation describe with only three kinds of codes into α helix pattern h, β sheet type pattern s, and other types pattern o. Especially useful for data mining of hyper-secondary structure like loop with complicated structure, it is useful for analysis of polymorphism of proteins with similar structures but amino acid sequences are very different.
Data type	Protein structure

Summary

The DCCP method (Dictionary of Conformational Code in Proteins) converts 3D information of protein X-ray crystal structure data to 1D information, and converts. Its conformation describe with only three kinds of codes into α helix pattern h, β sheet type pattern s, and other types pattern o. Especially useful for data mining of hyper-secondary structure like loop with complicated structure, it is useful for analysis of polymorphism of proteins with similar structures but amino acid sequences are very different.

Data type

Protein structure

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DPClus

Summary	DPClus is a graph clustering software, which makes it possible to detect and visualize clusters of proteins in interaction networks which mostly represent molecular biological functional units.
Data type	Protein-function

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FORTE

Summary	FORTE is a profile-profile comparison tool for protein fold recognition. Users can submit a protein sequence to explore the possibilities of structural similarity existing in known structures. Results are reported in the form of pairwise alignments.
Data type	Protein-structure

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GPCRs Interaction Partners

Summary	G-protein coupled receptor interaction partners (GRIP) is the web application to predict protein-protein interaction interfaces for G-protein coupled receptor oligomerization. This application provides predicted interfaces by Spatial Cluster Detection (SCD), Predicted interfaces are displayed interactively by using Jmol (cited from the original site).
Data type	Interaction GPCR

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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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HomeoRoq

Summary	HomeoRoq allows us to quantify ratios of homeolog expression levels in allopolyploid species, and links to genome sequences and raw reads of A. halleri subsp. gemmifera and A. lyrata subsp. petraea.HomeoRoq is a pipeline to detect statistically significant changes in the homeolog-specific expression ratios under different conditions using RNA-seq data
Data type	protein - amino-acid sequence

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MitoFates

Summary	MitoFates predicts mitochondrial presequence, a cleavable localization signal located in N-terminal, and its cleaved position.
Data type	protein - amino-acid sequence

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myPresto

Summary	myPresto is a molecular simulation system for structure-guided molecular development. myPresto consists of about 50 programs and databases. Namely, molecular dynamics simulation for proteins/DNA, protein-compound docking software, in-silico screening programs, conformer generator, file converting tools, and etc.For in-silico screening, chemical compound database is necessary. The compound database is available from BIRC/AIST.You can down load myPresto without charge from the web site of MEDALS and Laboratory of Protein Informatics, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University.
Data type	Protein-structure

Summary

myPresto is a molecular simulation system for structure-guided molecular development. myPresto consists of about 50 programs and databases. Namely, molecular dynamics simulation for proteins/DNA, protein-compound docking software, in-silico screening programs, conformer generator, file converting tools, and etc.For in-silico screening, chemical compound database is necessary. The compound database is available from BIRC/AIST.You can down load myPresto without charge from the web site of MEDALS and Laboratory of Protein Informatics, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University.

Data type

Protein-structure

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PAPIA

Summary	Tools for protein information analyses such as similar structure search, Homologous sequence search and Multiple sequence search by PC cluster.
Data type	Protein-structure

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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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POODLE

Summary	POODLE provides three types of disordered prediction according to length of the target disorder.POODLE-S and POODLE-L predict short disorder and long disorder regions,respectively. POODLE-W predicts which proteins are mostly disordered.
Data type	Protein-AminoAcid

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PRRN

Summary	PRRN is a multiple sequence alignment program by doubly nested randomized iterative method. PRRN accepts either nucleotide or protein sequences. PRRN repeatedly uses pairwise group-to-group alignment to improve the overall weighted sum-of-pairs score at each iterative step, where the pair weights are introduced to correct for uneven representations of the sequences to be aligned. The strategies of PRRN work most effectively for refining a crude alignment obtained by other more rapid methods, e.g. progressive alignment. (Summarized from the original site)
Data type	DNA, amino acid sequences

Summary

PRRN is a multiple sequence alignment program by doubly nested randomized iterative method. PRRN accepts either nucleotide or protein sequences. PRRN repeatedly uses pairwise group-to-group alignment to improve the overall weighted sum-of-pairs score at each iterative step, where the pair weights are introduced to correct for uneven representations of the sequences to be aligned. The strategies of PRRN work most effectively for refining a crude alignment obtained by other more rapid methods, e.g. progressive alignment. (Summarized from the original site)

Data type

DNA, amino acid sequences

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ScreenCap3

Summary	Screening of caspase-3 substrates and cleavage site prediction
Data type	protein - amino-acid sequence

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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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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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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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TMBETA-NET

Summary	TMBETA-NET is the program to discriminates outer membrane proteins and predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence.Ref.)http://unit.aist.go.jp/plan/enterprise-report/h16enterprise-report.pdf
Data type	Protein-motif

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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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WoLF PSORT

Summary	WoLF PSORT provides1) prediction of protein subcellular localization from amino acid sequence2) localization annotation for many proteins1) is available for arbitrary amino acid sequences. 2) is based on information from uniprot and the literature.
Data type	DNA-sequence , Nuclear genome encoded, Eukaryotic proteins

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