Ribobio > Support > Online Tools
In order to facilitate scientific researchers to do structure or sequence analysis, annotation, gene target prediction, and bioinformatics functional queries of various coding and non-coding RNA, we have listed useful online tools. RiboBio's informatics analysis platform integrates multiple bioinformatics databases, allowing researchers to personalize biodata on the web interface and create a personalized data analysis workflow. Please call +86 400-686-0075 or email marketing@ribobio.com for the service.
NCBI (National Center for Biotechnology Information) focuses on the basic and applied research in computing molecular biology with a group of computer scientists, molecular biologists, mathematicians, biochemists, experimental physicists, and structural biologists. It studies the organization of genes, analysis of sequences, and prediction of structures. The current research program include the detection and analysis of gene organization, repeat sequence forms, protein domains and structural units, the establishment of genetic maps of human genome, the mathematical models of kinetics of HIV infection, the analysis of sequence error effects in database searches, the development of a new alignment algorithm for database search and multiple sequence, the development of a non-redundant sequence database, a mathematical model for statistically significant evaluation of sequence similarity and a vector model for text retrieval. In addition, NCBI researchers continue to promote collaboration with other research institutes within NIH and research labs at many academies and governments.
Read More: https://www.ncbi.nlm.nih.gov/
miRBase 21.0
The miRBase sequence database, one of the authoritative data sources for miRNA research, is a comprehensive database that provides information on miRNA sequence data, annotations, and predicted gene targets. Currently, microRNA 21.0 is the latest version with a higher reliability, a total of 4,196 hairpin precursor sequences and 5441 mature miRNAs with some ambiguous and incorrectly annotated sequences have been removed.
Read More: http://www.mirbase.org/search.shtml
exoRBase
exoRBase is a repository of circular RNA (circRNA), long non-coding RNA (lncRNA) and messenger RNA (mRNA) derived from RNA-seq data analyses of human blood exosomes. Experimental validations from published articles are also included. exoRBase features the integration and visualization of RNA expression profiles based on standardized RNA-seq data spanning both normal individuals and patients with different diseases. exoRBase aims to collect and characterize all long RNA species in human blood exosomes by providing annotation, expression level and possible original tissues. exoRBase will aid researchers in identifying molecular signatures in blood exosomes and trigger new circulating biomarker discovery and functional implication for human diseases.
Read More: http://www.exorbase.org/
piRNABank
The piRNA database was created by Indian scientist SaiLakshmiS with his partners to preserve newly discovered piRNA sequences. It contains the most comprehensive piRNA sequence information, including nearly 20 million piRNA-related sequences of human, mouse and rat. After homologous sequence removal and genomic mapping, more than 100,000 piRNA sequence are detected with unique genome target sites. The database enables a variety of search methods for species and chromosomes, and it can also display each piRNA or piRNA cluster on a large genome map.
Read More: http://pirnabank.ibab.ac.in/
DIANA-LncBase
With a comprehensive annotation of miRNA targets on lncRNAs, DIANA-LncBase provides a database of experimentally supported and in silico predicted miRNA Recognition Elements (MREs) on lncRNAs in human and mice. The experimentally supported entries available in DIANA-LncBase correspond to > 5000 interactions, while the computationally predicted interactions exceed 10 million. It also maintains detailed information of each miRNA-lncRNA pair, such as external linkages, graphical mapping of transcript genomic locations, binding site characterization, lncRNA tissue expression, as well as MREs conservation and prediction scores.
Read More:www.microrna.gr/LncBase
Starbase is a powerful database commonly used in lncRNA/circRNA/microRNA research. With multiple sequencing data, Starbase integrates prediction software to help: 1. Find non-coding RNA (lncRNA, circRNA, etc) based on microRNA; 2. Find mRNA targets based on microRNA; 3. Find ceRNA regulatory molecules; 4. Find RNA-binding proteins.
Read More: http://starbase.sysu.edu.cn/
circRNADisease
circRNADisease is a human-supported database of circRNA and disease experiments and is an important source of knowledge for understanding the role of circRNA in human disease. Each entry contains circRNA and disease names, circRNA expression patterns, experimental techniques, circRNA partners, function descriptions of circRNAs, literature references and other annotations of circRNA.
Read More: http://cgga.org.cn:9091/circRNADisease/
Cancer-specific CircRNA Database
CSCD (Cancer-Specific CircRNA Database) is a database developed for cancer-specific loop proteins. CSCD collected available RNA sequencing (total RNA and rRNA depletion or Polya enrichment) data sets from 87 cancer cell samples, and conducted a comprehensive analysis with four popular algorithms – CIRI, FIDEXCIRC, CURCRNAX FIDER and CURCExpRever. It also collects CurcRNAs identified only in cancer samples. There are currently 272,152 cancer-specific loop proteins in CSCD.
Read More: http://gb.whu.edu.cn/CSCD/#
CycPediaV2
CycPediaV2 is an updated comprehensive database containing circRNA annotations of more than 150 RNA SEQ data sets from six different species, allowing users to search, browse and download circRNA with the expression features of various cells/tissues (including disease samples). In addition, the updated database incorporates a conservative analysis of CrCRNs between humans and mice. The web interface also contains a computational tool for comparing CyrRNA expression between samples.
Read More: http://www.picb.ac.cn/rnomics/circpedia/
GO Enrichment Analysis
After obtaining a specific gene set, the enrichment analysis of GO functional significance is able to determine the major biological functions of differentially expressed genes. GO ontology covers three major domains: Biological Process, Cellular Component and Molecular Function, referring to the biological process, cellular component, and molecular function of genes. The basic unit of GO is term, and each term corresponds to an attribute.
Read More: http://www.geneontology.org/
KEGG Enrichment Analysis
KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis identifies the most important biochemical metabolic pathways and signal transduction pathways involved in differentially expressed genes. KEGG is a major public database for Pathway. In organisms, different genes coordinate with each other to perform their biological functions, and Pathway analysis helps to further understand the biological functions of genes.
Read More: https://www.kegg.jp/
TANRIC Database
TANRIC Database is valuable tool for lncRNA research and an atlas of non-coding RNA in cancer, it characterizes the expression profiles of lncRNAs in large patient cohorts of 20 cancer types and more than 8,000 samples overall. TANRIC is an interactive data analysis and visualization platform that contains three categories of data: lncRNA annotation information, RNA-Seq data, and profiling data.
Read More: http://bioinformatics.mdanderson.org/main/TANRIC:Overview
FRNADB
FRNADB is a novel database service that carries a large number of non-coding transcripts, including annotated/non-annotated sequences from H-IV databases, non-coding and RNADB. A set of computational analyses was performed on the involved sequences, including RNA secondary structure motif discovery, EST support evaluation, cis-regulatory element search, protein homology search.
Read More: http://togodb.biosciencedbc.jp/togodb/view/frnadb_summary#en
Predict circRNA Binding Target – CircInteractome
CircInteractome predicts the binding sites of the known 109 RNA-binding protein datasets with the circRNA in circbase, and predicted potential binding sites for miRNAs to circRNA using Targetscan software. It supports operations such as circRNA molecular search, circRNA-binding protein prediction, PCR primer design, and siRNA interference sequence design.
Read More: https://circinteractome.nia.nih.gov/
miRNA Target Gene Prediction
Findtar3: http://bio.sz.tsinghua.edu.cn/
TargetScan: http://www.targetscan.org/
miRDB: http://mirdb.org/miRDB/index.html
RNA22v2: https://cm.jefferson.edu/rna22v2/
microRNA.org: http://www.microrna.org/microrna/home.do
tRNA Database
PlantRN: http://plantrna.ibmp.cnrs.fr/
tRFdabase: http://genome.bioch.virginia.edu/trfdb/
tRNAdb: http://trna.bioinf.uni-leipzig.de/DataOutput/
tRNADB-CE: http://trna.ie.niigata-u.ac.jp/cgi-bin/trnadb/index.cgi
.tRNA Naming: http://www.genenames.org/cgi-bin/genefamilies/set/478
Venn Diagram is a series of circles that overlap to show the possibilities of various data sets. It represents the intersection and different sets among up to 30 sets of data.
BioVenn: http://www.cmbi.ru.nl/cdd/biovenn/index.php
Venn: http://bioinformatics.psb.ugent.be/webtools/Venn/
VENNY: http://bioinfogp.cnb.csic.es/tools/venny/index.html
Venn Diagram Plotter: http://omics.pnl.gov/software/venn-diagram-plotter
VennDiagram: R package http://cran.r-project.org/web/packages/VennDiagram/index.html
Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
http://www.ensembl.org/index.html
piRNApredictor
piRNApredictor predicts piRNA sequence information, and identifies non-model biological piRNA without relying on genomic data. The high-precision prediction results of piRNA have important theoretical significance for research on epigenetics, regulatory networks and piRNA functions. piRNApredictor has been used in piRNA research in pigs by international research institutions.
https://omictools.com/pirnapredictor-tool
RNAfold Web Server
RNAfold web server predicts the secondary structure of RNA molecules. By entering the RNA sequence that needs to study, the system will calculate the results to show different structural expressions.
http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi
NRED
NRED, built by John Mattick Lab, provides gene expression information for thousands of long ncRNAs in human and mouse.
http://jsm-research.imb.uq.edu.au/nred/
LncRNADisease database
LncRNADisease (lncRNA and disease database ) contains more than 160 diseases associated with long non-coding RNAs. It has also built a bioinformatics platform that integrates tools for predicting novel lncRNA-disease associatons.
http://www.cuilab.cn/lncrnadisease
CyrRNADB Database
CyrRNADB is a comprehensive database of circular RNA molecules in humans. It is freely available for non-commercial use. The latest version of this circRNA database contains 32,914 annotated exonic circRNAs, and can be a valuable resource for large-scale studies of circRNA, especially in humans.
http://202.195.183.4:8000/circrnadb/circRNADb.php
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
https://www.uniprot.org/
LNCipedia
LNCipedia offers a comprehensive annotation of the sequence and structure of long-chain non-coding RNA in human.
http://www.lncipedia.org/db
ExcOctA
Exosomes are 30-150nm membrane vesicles of endocytic origin secreted by most cell types in vitro. ExoCarta is an exosome database to provide the contents that were identified in exosomes in multiple organisms.
http://www.exocarta.org/
Vesiclepedia
Vesiclepedia is a database dedicated to the study of extracellular vesicles. It involves 33 species and 538 provenance researches, and themiRNAs/mRNA/protein/fat found in apoptotic bodies, microvesicles, exosomes and other vesicles are included.
Read More: http://www.microvesicles.org/
EVpedia
EVpedia is a database of extracellular vesicles in prokaryotic and eukaryotic organisms, containing miRNA, mRNA, m proteins, lipids, metabolites and their corresponding markers found in different vesicle (exosomes included) studies. Furthermore, EVpedia provides data analysis and functional annotation.
http://student4.postech.ac.kr/evpedia2_xe/xe/
The Functional lncRNA Database
The Functional lncRNA Database is a mammalian lncRNA database, with the majority of these lncRNAs are from human, mouse and rat. To search for a specific lncRNA, you can either type the lncRNA name in the search box and select the appropriate variety or browse all lncRNAs once.
http://www.valadkhanlab.org/database
lncRNAdb
lncRNAdb provides a comprehensive annotation of biologically functional long-chain non-coding RNA, it is built by the John Mattick Lab.
NONCODE provides comprehensive annotation for long non-coding RNA, including expression and lncRNA function predicted by the team's ncFANs computer software.
http://www.microvesicles.org/
GeneCards v3
GeneCards is a searchable integrative database that provides concise genome-related information for all known and predicted human genes.
http://www.genecards.org/
NCBI/ BLAST
NCBI/ BLAST is a common tool for sequence analysis. BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Read More: https://blast.ncbi.nlm.nih.gov/Blast.cgi
Linc2GO
Linc2GO is a web resource that aims to provide comprehensive functional annotations for human lincRNA. MicroRNA-mRNA and microRNA-lincRNA interaction data were integrated to generate lincRNA functional annotations based on the 'competing endogenous RNA hypothesis'.
Read More: https://omictools.com/linc2go-tool
lncLocator: long non-coding RNA
lncLocator is developed by the Pattern Recognition and Bioinformatics Group of Shanghai Jiaotong University to predict the localization of lncRNA in subcellular cells.
Read More: http://www.csbio.sjtu.edu.cn/bioinf/lncLocator/
UCSC Genome Browser
The UCSC Genome Browser contains genome sketches of multiple species including humans, mice and rats, and is updated in sync with ENCODE. With an array of online analysis tools, users are able to reliably and quickly browse any part of the genome, and acess the genomic annotation information related for free download.
http://genome.ucsc.edu/
TCGA
TCGA is a joint database of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), which has produced a comprehensive, multidimensional map of key genomic changes in 33 cancer types. TCGA is publicly available with more than two genomic data, and it has helped to diagnose, treat and prevent cancers.
https://cancergenome.nih.gov/
circNet
circNet generates an integrated interaction network between circRNAs, miRNAs and mRNAs.
http://circnet.mbc.nctu.edu.tw/
circBaae
circBase is used to explore circRNA information.
http://www.circbase.org/
CircPro
CircPro is an automated high-throughput data analysis pipeline capable of detecting circRNAs, predicting their protein-coding potential and discovering junction reads from Ribo-Seq data.
http://bis.zju.edu.cn/CircPro/
Cystoscape
Cytoscape is an open source software platform for visualizing and analyzing complex networks. It creates molecular interaction networks.
Read More: http://www.cytoscape.org/index.html
catRAPID
catRAPID predicts the algorithm for large-scale RNA-protein interactions.
http://big.crg.cat/gene_function_and_evolution/services/catrapid
Chord Diagram
A chord diagram is a representation of the relationship between a set of units with mutual connections. The thickness of the lines indicates the degree of association in gene fusion, co-expression, and protein interaction.
http://mkweb.bcgsc.ca/tableviewer/visualize/
ceRNA: circNet
circNet is a ceRNA functional research database, using 464 RNA-seq sequencing data for new circRNA predictions and genome annotations, for the calculation of the known and predicted circRNA expression, and the construction of a circRNA-miRNA-gene regulatory network.
Cluster Diagram
Cluster analysis is an unsupervised classification method commonly used for high-throughput data. The similarity between the samples is calculated by the feature set to build a similarity matrix and cluster the same or similar types of samples according to certain principles, so as to directly observe the difference between the samples.
http://www2.heatmapper.ca/expression/