Bioinformatics Online Tools

In order to facilitate structure or sequence analysis, annotation, gene target prediction, function query, and other bioinformatic contents for various types of coding and non-coding RNAs, we have assembled the most commonly used online tools as shown below.

Databases

ToolsDescriptionWebsite
NCBINational Center for Biotechnology Information.

Bioinformatics Online Tools

ExoCarta exosome databaseDatabase of exosomes, providing content identified in exosomes of multiple organisms.

Bioinformatics Online Tools

Vesiclepedia Extracellular vesicle databaseDatabase for extracellular vesicle research.

Bioinformatics Online Tools

circRNADiseaseDatabase manually supported by circRNA and disease experiments.

Bioinformatics Online Tools

miRBase 21.0A comprehensive database that provides information including miRNA sequence data, annotations, predicted gene targets, etc.

Bioinformatics Online Tools

piRNABankpiRNABank contains the most comprehensive piRNA sequence information available, including nearly 20 million piRNA-related sequences from species of human, mouse and rat.

Bioinformatics Online Tools

StarbaseStarbase is commonly used in lncRNA/circRNA/microRNA research, etc.

Bioinformatics Online Tools

CSCD cancer-associated circRNACSCD (cancer-specific circRNA database) is a database developed for cancer-specific cyclins.

Bioinformatics Online Tools

FRNADBIt hosts a large number of non-coding transcripts, including annotated/non-annotated sequences from the H-IV database, non-coding and RNADB.

Bioinformatics Online Tools

The Functional lncRNA DatabaseA database of mammalian long-stranded non-protein-coding transcripts.

Bioinformatics Online Tools

CIRCpedia (v2)An updated and comprehensive database containing circRNA annotations for over 150 RNA SEQ datasets from 6 different species.

Bioinformatics Online Tools

LncRNADisease databaseThe lncRNA and disease database (LncRNADisease), a database that contains more than 160 diseases associated long non-coding RNAs, and bioinformatics tool integration to predict the relationship between new human long non-coding RNAs and diseases.

Bioinformatics Online Tools

NONCODEA well-known database for non-coding RNA research, providing comprehensive annotation of long-stranded non-coding RNAs.

Bioinformatics Online Tools

GeneCards v3GeneCards is a searchable, integrated human gene database that provides concise genome-related information on all known and predicted human genes.

Bioinformatics Online Tools

TCGATCGA is a collaborative database of the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) that produces comprehensive and multidimensional maps of key genomic changes in 33 cancers.

Bioinformatics Online Tools

circRNA Search DatabaseIt is used to retrieve circRNA information.

Bioinformatics Online Tools

exoRBase 2.0exoRBase is a repository of circulating RNA (circRNA), long-stranded non-coding RNA (lncRNA) and messenger RNA (mRNA) derived from RNA SEQ data analysis of human blood exosomes, which also includes experimental validations of published literatures.

Bioinformatics Online Tools

DIANA-LncBaseDIANA-LncBase provides comprehensive annotation of miRNA targets on lncRNAs, preserving experimentally validated and computationally predicted miRNA recognition elements on human and mouse lncRNAs for the entire transcriptome.

Bioinformatics Online Tools

UniProt protein sequence and functionUniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource for protein sequence and functional information.

Bioinformatics Online Tools

LNCipediaIt provides comprehensive annotation of the sequence and structure of long-stranded human non-coding RNAs.

Bioinformatics Online Tools

miRDBmiRDB is an online database for miRNA target prediction and functional annotations.

Bioinformatics Online Tools

Bioinformatics Analysis

ToolsDescriptionWebsite
GO Enrichment AnalysisThe GO functional significance enrichment analysis is able to identify the major biological functions performed by a specific set of differential genes.

Bioinformatics Online Tools

KEGG enrichment analysisThe KEGG significant enrichment analysis identifies the most essential biochemical metabolic pathways and signal transduction pathways involved in differentially expressed genes.

Bioinformatics Online Tools

Prediction of circRNA binding targets - CircInteractomeIt performs operations such as circRNA molecule search, circRNA binding protein prediction, PCR primer design and siRNA interference sequence design.

Bioinformatics Online Tools

NCBI/ BLASTA tool commonly used for sequence analysis.

Bioinformatics Online Tools

RNAfold web serverIt predicts the secondary structure of RNA molecules.

Bioinformatics Online Tools

CircProCircPro is an automated high-throughput data analysis process that detects circRNAs, predicts their protein-coding potential and discovers contiguous reads for Ribo sequencing data.

Bioinformatics Online Tools

TargetScanIt searches predicted microRNA targets in mammals.

Bioinformatics Online Tools

Primer design

ToolsDescriptionWebsite
Primer3PlusA Primer selection tool for DNA sequences.

Bioinformatics Online Tools

Primer-BLASTA tools used to define specific primers for PCR templates.

Bioinformatics Online Tools

* Only for research. Not suitable for any diagnostic or therapeutic use.
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