RNAsnp Web Server::Submit. MiRmap. R3D Align. Clotelab: RNA Inverse Folding: Home. The RNA inverse folding problem is the problem, given a target secondary structure in dot bracket notation, of determining one or more RNA sequences, whose minimum free energy (MFE) structure is the target structure. Here, the MFE structure is computed using RNAfold from the Vienna RNA Package. In addition, the user may provide sequence constraints, stipulating that certain positions be occupied by specific nucleotides, or that (for instance) the solution sequence has a GC-content within a certain user-specified range.
This website provides access to two algorithms for the inverse folding problem: Synthetic Design RNA Synthetic design. Simple 3-step pipeline to design synthetic RNAs that fold into the consensus structure of a user-selected Rfam family. RNA-CPdesign RNA-CPdesign. Corresponding to the hybridization which includes intra-molecular structure of the first sequence, along with hybridization between first and second sequences. Modena structures RNA-SSD structures RNA-SSD Test Set C. Page Redirection To SPARCS. RNAtips. Vienna RNA Package 2 - Source Code. There should rarely be a good reason to use any but the latest version of our software.
However if you want to look up the old bugs, here's a list with most of the older releases for download: 2.0.x ViennaRNA Package v2.0.7 (tar.gz, SourceCode) [3.8MB]ViennaRNA Package v2.0.6 (tar.gz, SourceCode) [3.8MB]ViennaRNA Package v2.0.5 (tar.gz, SourceCode) [3.8MB]ViennaRNA Package v2.0.4 (tar.gz, SourceCode) [3.8MB]ViennaRNA Package v2.0.3b (tar.gz, SourceCode) [3.8MB]ViennaRNA Package v2.0.3 (tar.gz, SourceCode) [3.8MB]ViennaRNA Package v2.0.2 (tar.gz, SourceCode) [3.8MB]ViennaRNA Package v2.0.1 (tar.gz, SourceCode) [3.8MB]ViennaRNA Package v2.0.0 (tar.gz, SourceCode) [3.8MB]
You are being redirected to the Freiburg RNA Tools. CARNA is a tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures. Alternatively, you can also provide base pair probability matrices (dot plots in .ps format) or fixed structures (as annotation in the FASTA alignment) for your sequences.
If you provide fixed structures, only those structures and not the entire ensemble of possible structures is aligned. In contrast to LocARNA, CARNA does not pick the most likely consensus structure, but computes the alignment that fits best to all likely structures simultaneously. Hence, CARNA is particularly useful when aligning RNAs like riboswitches, which have more than one stable structure. Also, CARNA is not limited to nested structures, but is able to align arbitrary pseudoknots. For papers describing the tool refer to the reference section below. QIIME. Galaxy. Jalview - Java alignment editor. What is Jalview ? | jalview.aegir.lifesci.dundee.ac.uk. ?utm_source=dlvr. KOSMOS-Korea SKKU Morph Server.
Introduction KOSMOS is the first web server to provide the structural biology community with both harmonic and anharmonic analyses of macromolecular structures including DNA, RNA, and Proteins. Online users can request thermal fluctuation study or transient pathway generation by simply submitting PDB ID or uploading personal data files through the query page. All the simulation outputs have been deposited into NMA and ENI database where most of data are disclosed to the public unless users request to limit accessibility to their data. Users can also enjoy versatility of KOSMOS through advanced query by utilizing several unique applications of elastic network models for their own purpose. Harmonic - Normal Mode Analysis (NMA) Normal mode analysis (NMA) is a useful tool to understand the harmonic behaviors (thermal fluctuations) of a macromolecule around its equilibrium.
Anharmonic (Pathway Generation) - Elastic Network Interpolation (ENI) Getting Start! PsRobot: Plant Small RNA Analysis Toolbox - Powered by omicslab. PsRobot is designed to analyze batch of plant small RNA data. The online version of psRobot has two modules: The stem-loop small RNA prediction (try it out) module can identify stem-loop shaped smRNAs, including their expression in major plant smRNA biogenesis gene mutants and smRNA associated protein complexes to give clues to the smRNA generation and functional processes, their genome locations and precursor sequences. The second module, small RNA target prediction (try it out) module, can return target prediction results of smRNAs, including smRNA target list, target multiplicity, target site conservation and biological data support, such as degradome data and target expression data in small RNA biogenesis mutants.
PsRobot also features a local version. The local programs offers a larger capacity for input data size and has the function to incorporate user-uploaded degradome data. Please go to the Software section for details. Start?utm_source=dlvr. The goal of QGRS-H Predictor is to map and analyze phylogenetically conserved putative Quadruplex forming 'G'-Rich Sequences (QGRS) in the mRNAs, ncRNAs and other nucleotide sequences -e.g. Promoter and Telomeric and gene flank regions. The putative G-quadruplexes are identified using the following motif: Where x = # guanine tetrads in the G-quadruplex and y1, y2, y3 = length of gaps QGRS-H Predictor web tool generates information on composition and distribution of putative homologous G-quadruplexes in semi-globally aligned nucleotide sequences based on published algorithms.
Enter 2 sequences in the input area to the left to run an analysis. The program is limited to mRNA sequences less than 10,000 bases in length. Quick-start tutorialProject background Please cite: Menendez, C., Frees, S., and Bagga, P. (2012) QGRS-H Predictor: A Web Server for Predicting Homologous Quadruplex forming G-Rich Sequence Motifs in Nucleotide Sequences. TaxMan: Inspect your rRNA amplicons and taxa assignments. Brandt, B.W., Bonder, M.J., Huse, S.M. and Zaura, E. (2012) TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage. . CORE: Griffen, A.L., Beall, C.J., Firestone, N.D., Gross E.L., DiFranco, J.M., Hardman, J.H., Vriesendorp, B., Faust, R.A., Janies, D.A. and Leys, E.J. (2011) CORE: A phylogenetically-curated 16S rDNA database of the core oral microbiome. PLoS ONE 6(4): e19051. HOMD: Chen, T., Yu, W-Han, Izard, J., Baranova, O.V., Lakshmanan, A., Dewhirst, F.E. (2010) The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.
Database, Vol. 2010 Database 2010:baq013. Greengenes: DeSantis, T. Z., Hugenholtz P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber T. ,Dalevi, D., Hu, P. and Andersen, G.L. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Vaginal 16S reference package, by Hoffman, N., Srinivasan, S. and Matsen, M. Home Page. Rtips. SAVoR: Sequencing Annotation and Visualization of RNA structures. Gallery An example showing the double-stranded RNA (dsRNA) read coverage along a tRNA from D. melanogaster (FlyBase ID: FBtr0071626). The orange-red color scheme is used here. An example showing the structure score (log-ratio of dsRNA-seq to ssRNA-seq read coverage) along the protein-coding F54E12.3 transcript in C. elegans.
The blue-red color scheme is used here with default thresholds. An example showing the dsRNA endpoint abundance along a U2 snRNA from D. melanogaster (FlyBase ID: FBtr0074208). An example showing 3 SNPs from a 300bp region of intron 1 of the FTO gene (chr16:53820377-53820676). An example showing the conservation (phyloP46wayAll) score along mir-105. Help topics SAVoR generates high-quality secondary structure models with various sequencing-oriented annotation options such as read coverage, endpoint locations, and SNP calls.
Four input types are currently supported: Rfam ID (e.g. RefSeq/SGD/TAIR ID (e.g. Rfam: Directly uses the specified Rfam structure. 1. 2. 3. 4. F. RNA Characterization of Secondary Structure Motifs Database (RNA CoSSMos) MINAS - UZH. MirDIP: microRNA Data Integration Portal. MirDIP integrates twelve microRNA prediction datasets from six microRNA prediction databases, allowing users to customize their microRNA target searches. Combining microRNA predictions allows users to obtain more robust target predictions, giving you more confidence in your microRNA targets. See the instruction page for more information. All contents copyright , Jurisica Lab, Ontario Cancer Institute, Princess Margaret Hospital/UHN. Last modified January, 2012. (Version 1.1.2) All downloads and use of this database are subject to the following terms.
Permission to use, copy, and modify this database hereby granted to all academic and not-for-profit institutions without fee, provided that name of organization and author appear in all copies of the database. Reference: Shirdel EA, Xie W, Mak TW, Jurisica I, 2011 NAViGaTing the Micronome . DIANA LAB - Tarbase. VIRsiRNAdb. FASTR3D: A Fast and Accurate Search Tool for RNA 3D Structures. The Elements of Bioinformatics.
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