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16S and 23S Ribosomal RNA Mutation Database
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| Search for information about mutated positions in 16S and 16S-like ribosomal RNA and 23S and 23S-like ribosomal RNA and the identity of each alteration.
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3D rRNA modification maps database
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| A database of maps showing the sites of modified rRNA nucleotides in three-dimensional models.
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5S Ribosomal RNA Database
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| Search for information on nucleotide sequences of 5S rRNAs and their genes.
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A software tool-box for analysis of regulatory RNA elements
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| Identify regulatory RNA elements.
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ACTIVITY -- A distributed and intelligent database for the activities of the functional sites in DNA and RNA.
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| Search for activities of the functional sites in DNA and RNA. |
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ARED Organism -- expansion of ARED reveals AU-rich element cluster variations between human and mouse
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| View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.
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Aptamer database
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| Search for comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods.
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BLAT Search Genome
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| Quickly find sequences of 95% and greater similarity of length 40 bases or more for DNA or 80% and greater similarity of length 20 amino acids or more for protein in a genome. |
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BPS -- RNA Base-Pair Structures Database
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| Find quantitative information on the spatial arrangements of interacting RNA bases.
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CPC -- Coding Potential Calculator
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| Assess the protein-coding potential of transcripts using sequence features and support vector machine.
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Compilation of tRNA sequences and sequences of tRNA genes
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| Search for sequence information on tRNA genes and tRNA.
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CorreLogo -- an online server for 3D sequence logos of RNA and DNA alignments
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| Generate a three-dimensional representation for a given RNA or DNA sequence alignment.
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DED -- Database of Evolutionary Distances
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| Search, store and analyze evolutionary distances among homologous genes in different organisms. |
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Database for mobile group II introns
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| Search for comprehensive information about group II introns.
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GRSDB2 -- a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences
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| Search for information on composition and distribution of putative Quadruplex forming 'G'-Rich Sequences (QGRS) in the alternatively processed (alternatively spliced or alternatively polyadenylated) mammalian pre-mRNA sequences.
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GtRDB -- Genomic tRNA Database
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| Search for information on computationally predicted tRNA genes in various genomes.
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GtRNAdb -- Genomic tRNA Database
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| Find information about computationally identified transfer RNA genes.
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HIV Sequence Database
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| Search for annotated HIV and related SIV DNA and translated amino acid sequences.
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HuSiDa -- the human siRNA database -- an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells
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| Search for sequences of published functional siRNA molecules targeting human genes and associated information.
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IRESdb -- the Internal Ribosome Entry Site database
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| Search for sequence and other information about internal ribosome entry sites (IRES).
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IRESite -- The database of experimentally verified IRES structures
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| Search for information about the experimentally studied IRES (Internal Ribosome Entry Site) segments.
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ITS2 Database II -- homology modelling RNA structure for molecular systematics
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| Model ITS2 secondary structures based on sequences with known structures.
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LeARN -- a platform for detecting, clustering and annotating non-coding RNAs
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| A software package which handles the complete process of ncRNA annotation by integrating the layers of automatic detection and human curation.
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Locomotif -- from graphical motif description to RNA motif search
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| Program that allows for the visual design of RNA motifs.
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MAGNOLIA -- multiple alignment of protein-coding and structural RNA sequences
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| An advanced multiple alignment program suite for nucleic sequences.
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MGAlignIt -- a web service for the alignment of mRNA/EST and genomic sequences
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| Align mRNA or expressed sequence tags (EST) and genome sequences. |
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MODOMICS -- database of RNA modification pathways
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| Search for comprehensive information on RNA modification.
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MeRNA -- a database of metal ion binding sites in RNA structures
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| Search for metal binding sites identified in RNA 3D structures available from the PDB and Nucleic Acid Database. |
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MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.
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| Distinguish between real and pseudo microRNA precursors |
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MicroInspector -- a web tool for detection of miRNA binding sites in an RNA sequence
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| Detect miRNA binding sites in RNA sequences.
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Multiple sequence alignment of prokaryotic 16S rDNA
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| Examine the comprehensive database of 16S rDNA prokaryotic multiple sequence alignment.
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NAST -- a multiple sequence alignment server for comparative analysis of 16S rRNA genes
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| Compare 16s rRNA genes using multiple sequence alignment.
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NONCODE v2.0 -- decoding the non-coding
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| Search for information to analyze non-coding RNAs.
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NRED -- Non-coding RNA Expression Database
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| Find gene expression information about long, non-protein-coding RNAs in human and mouse.
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PACdb -- PolyA Cleavage Site and 3'-UTR Database
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| Search for putative 3'-processing sites and 3'-UTR sequences for multiple model organisms. |
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PLMItRNA -- A database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes
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| Retrieve information on the distribution of tRNA molecules and genes in mitochondria of green plants (higher plants and green algae) and Cryptophyta, Rhodophyta and Stramenopiles algae. |
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PRFdb -- Programmed Ribosomal Frameshift Database
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| A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals.
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Plant snoRNA database
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| Search for comprehensive information on small nucleolar RNAs in plants.
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PolyA_DB -- A database for mammalian mRNA polyadenylation
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| Search for information regarding polyadenylation in vertebrate genes.
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PromEC -- A database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites
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| Search for information on E. coli mRNA promoter sequences and transcriptional start sites. |
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PseudoBase -- structural information on RNA pseudoknots
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| Search for information on RNA pseudoknots.
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PseudoBase++ -- An Extension of PseudoBase
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| Find information about pseudoknots.
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R-Coffee -- Mulitiple RNA Sequence Alignment
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| Web server for accurately aligning noncoding RNA sequences.
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REDIdb -- the RNA editing database
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| Search for information on various RNA editing events.
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RIDOM -- Ribosomal Differentiation of Medical Micro-organisms Database
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| Differentiate medical microorganisms based on partial small subunit ribosomal DNA (16S rDNA) sequence. |
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RISP -- RNA-Interaction Site Prediction
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| A web-based server for prediction of RNA-binding sites in proteins.
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RISSC -- a novel database for ribosomal 16S–23S RNA genes spacer regions
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| Search for DNA sequence data from the 16S–23S ribosomal spacers present in most prokaryotes and organelles (e.g. mitochondria and chloroplasts).
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RNAdb —- a comprehensive mammalian noncoding RNA database
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| Search for information on experimentally studied mammalian non-coding RNAs (ncRNAs), including many associated with diseases and/or developmental processes.
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RefSeq -- Reference Sequence database
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| Find sequences representing genomes, transcripts, and proteins. |
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RegRNA -- an integrated web server for identifying regulatory RNA motifs and elements
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| Identify both sequence and structure homologs of Regulatory RNA motifs and elements.
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Regulatory noncoding RNAs database
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| Search for sequences and functions of noncoding RNA in various organisms.
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Rfam -- An non-coding RNA family database
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| Search for multiple sequence alignments and covariance models representing non-coding RNA families.
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RibEx -- a web server for locating riboswitches and other conserved bacterial regulatory elements
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| Search sequences of known and predicted riboswitches and other conserved bacterial regulatory elements.
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Ribosomal Internal Spacer Sequence Collection
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| Search for information on ribosomal 16S-23S spacer.
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SARSA -- a web tool for structural alignment of RNA using a structural alphabet
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| Align two or more RNA tertiary structures.
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SVC -- structured visualization of evolutionary sequence conservation
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| Perform detailed analysis and visualization of evolutionary sequence conservation in complex vertebrate genes. |
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Small RNA Database
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| Search for sequences and other information on small RNAs.
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Sno/scaRNAbase -- a curated database for small nucleolar RNAs and cajal body-specific RNAs
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| Search for annotated information on small nucleolar RNAs and cajal body-specific RNAs in many different organisms.
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SnoReport -- computational identification of snoRNAs with unknown targets
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| Identify small nucleolar RNAs with unknown targets.
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Software.ncrna.org -- web servers for analyses of RNA sequences
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| A portal site of web servers and software tools for sequence/structure analysis of non-coding RNAs.
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TACT -- Transcriptome Auto-annotation Conducting Tool of H-InvDB
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| Conduct functional annotation of mRNA transcripts. |
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TFAM -- an online tRNA function classifier
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| Classify the function of tRNAs.
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TarBase -- miRNA Targets Database
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| Search for targets of miRNA gene silencing in animals, plants and viruses.
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TargetRNA -- a tool for predicting targets of small RNA action in bacteria
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| Identify targets of small (non-coding) RNA action.
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Tcoffee@igs -- A web server for computing, evaluating and combining multiple sequence alignments
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| Conduct and evaluate multiple sequence alignments for protein, DNA and RNA. |
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The ERPIN Server -- An Interface to Profile-based RNA Motif Identification
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| Identify related RNA sequences based on RNA sequence alignment.
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The European ribosomal RNA database
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| Search for comprehensive information on SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences, structures, taxonomy, and literature.
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RDP -- The Ribosomal Database Project
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| Provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. |
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The Small Subunit rRNA Modification Database
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| Search for post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs.
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The guide RNA database
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| Search for published information on guide RNAs.
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The microRNA Registry
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| To obtain unique names for novel miRNA genes prior to publication of results
and to search sequence information of published miRNAs.
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The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
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| Search for tRNA genes and snoRNA genes in genomic sequences. |
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The tmRNA website -- reductive evolution of tmRNA in plastids and other endosymbionts
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| To search for sequences, alignments, secondary structures and other information on tmRNA. |
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Tools for the automatic identification and classification of RNA base pairs
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| Classify and visualize RNA structures.
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Transterm -- A database of mRNAs and translational control elements
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| Search for elements and biologically relevant regions in mRNAs that control translation. |
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UTRdb and UTRsite -- Specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs.
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| Search for the 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs.
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ViTa -- prediction of host microRNAs targets on viruses
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| Search for curated information of the known virus miRNA genes and the known/putative target sites of human, mice, rat and chicken miRNAs. |
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Yeast snoRNA Database
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| Search for information for small nucleolar RNAs (snoRNAs)in yeast. |
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dbRES -- a web-oriented database for annotated RNA editing sites
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| Search for information of published RNA editing sites.
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fRNAdb -- databases to support mining and annotation of functional RNAs
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| Search for information on non-annotated/unannotated non-coding mRNA transcripts.
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miR2Disease -- microRNA Disease Database
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| Search for information about diseases caused by miRNA deregulation.
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miRNAMap 2.0 -- genomic maps of microRNAs in metazoan genomes
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| Search for information on the published and predicted miRNA in vertebrate genomes.
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miROrtho -- miRNA Orthology Database
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| Search for animal microRNA genes.
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miRU -- an automated plant miRNA target prediction server
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| Identify potential plant miRNA targets.
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miRecords -- microRNA-target Interactions Database
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| Search for predicted miRNA targets.
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ncRNAdb -- Noncoding regulatory RNAs database
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| Search for sequence and other information about noncoding regulatory RNAs.
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probeBase -- An online resource for rRNA-targeted oligonucleotide probes
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| Search for published rRNA-targeted oligonucleotide probe sequences. |
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pssRNAMiner -- a plant short small RNA regulatory cascade analysis server
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| Identify both the clusters of phased small RNAs as well as the potential phase-initiator.
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sRNAMap -- small non-coding RNA maps
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| Findgenomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes.
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snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
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| Search for information on human C/D box and H/ACA box small nucleolar RNAs (snoRNAs), and small Cajal body-specific RNAs (scaRNAs).
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tRNA-SE Search tool
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| Search for tRNA genes in a genomic sequence.
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tRNADB-CE -- tRNA Gene Database Curated by Experts
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| Find information about prokaryotic tRNA genes.
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tRNAdb -- tRNA sequences and genes database
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| Find information about transfer RNA.
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tmRDB -- A tmRNA database
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| Search for aligned, annotated and phylogenetically ordered sequences related to structure and function of tmRNA.
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