Included are RNA motif search programs to help analyze recurrent subsets of nucleotide arrangements in secondary or tertiary structure.

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CopraRNA and IntaRNATool Content

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CopraRNA and IntaRNA webserver tools: CopraRNA is a tool for sRNA target prediction, while IntaRNA enables the prediction of RNA-RNA interactions.

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ERPINTool Content

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ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

Freiburg RNA ToolsTool Content

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The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.

IBM Bioinformatics and Pattern Discovery GroupTool Content

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Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

ITS2Tool Content

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The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

MicroInspectorTool Content

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MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.

MoD ToolsTool Content

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Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

QGRS MapperTool Content

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Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

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