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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
| Tools | Description | Website |
| NCBI | National Center for Biotechnology Information. |
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| ExoCarta exosome database | Database of exosomes, providing content identified in exosomes of multiple organisms. |
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| Vesiclepedia Extracellular vesicle database | Database for extracellular vesicle research. |
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| circRNADisease | Database manually supported by circRNA and disease experiments. |
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| miRBase 21.0 | A comprehensive database that provides information including miRNA sequence data, annotations, predicted gene targets, etc. |
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| piRNABank | piRNABank contains the most comprehensive piRNA sequence information available, including nearly 20 million piRNA-related sequences from species of human, mouse and rat. |
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| Starbase | Starbase is commonly used in lncRNA/circRNA/microRNA research, etc. |
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| CSCD cancer-associated circRNA | CSCD (cancer-specific circRNA database) is a database developed for cancer-specific cyclins. |
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| FRNADB | It hosts a large number of non-coding transcripts, including annotated/non-annotated sequences from the H-IV database, non-coding and RNADB. |
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| The Functional lncRNA Database | A database of mammalian long-stranded non-protein-coding transcripts. |
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| CIRCpedia (v2) | An updated and comprehensive database containing circRNA annotations for over 150 RNA SEQ datasets from 6 different species. |
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| LncRNADisease database | The 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. |
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| NONCODE | A well-known database for non-coding RNA research, providing comprehensive annotation of long-stranded non-coding RNAs. |
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| GeneCards v3 | GeneCards is a searchable, integrated human gene database that provides concise genome-related information on all known and predicted human genes. |
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| TCGA | TCGA 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. |
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| circRNA Search Database | It is used to retrieve circRNA information. |
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| exoRBase 2.0 | exoRBase 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. |
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| DIANA-LncBase | DIANA-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. |
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| UniProt protein sequence and function | UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource for protein sequence and functional information. |
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| LNCipedia | It provides comprehensive annotation of the sequence and structure of long-stranded human non-coding RNAs. |
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| miRDB | miRDB is an online database for miRNA target prediction and functional annotations. |
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Bioinformatics Analysis
| Tools | Description | Website |
| GO Enrichment Analysis | The GO functional significance enrichment analysis is able to identify the major biological functions performed by a specific set of differential genes. |
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| KEGG enrichment analysis | The KEGG significant enrichment analysis identifies the most essential biochemical metabolic pathways and signal transduction pathways involved in differentially expressed genes. |
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| Prediction of circRNA binding targets - CircInteractome | It performs operations such as circRNA molecule search, circRNA binding protein prediction, PCR primer design and siRNA interference sequence design. |
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| NCBI/ BLAST | A tool commonly used for sequence analysis. |
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| RNAfold web server | It predicts the secondary structure of RNA molecules. |
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| CircPro | CircPro is an automated high-throughput data analysis process that detects circRNAs, predicts their protein-coding potential and discovers contiguous reads for Ribo sequencing data. |
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| TargetScan | It searches predicted microRNA targets in mammals. |
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Primer design
| Tools | Description | Website |
| Primer3Plus | A Primer selection tool for DNA sequences. |
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| Primer-BLAST | A tools used to define specific primers for PCR templates. |
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* Only for research. Not suitable for any diagnostic or therapeutic use.
