DNA Structure Analysis Tools

banana

• Description : banana is a tool for predicting and plotting B-DNA bending and curvature. The banana algorithm predicts B-DNA, normal DNA, double helix bending utilizing the Goodsell & Dickerson method by computing the extent of local bending and macroscopic curving at each point of a DNA sequence.

Bioinformatics Toolkit

• Description : Bioinformatics Toolkit is a web-server consisting of a collection of sequence analysis tools.
  Search tools: HHblits, HHpred, HMMER, PatternSearch, ProtBLAST, PSI-BLAST
  Alignment: Alignmentviewer, Clustal Omega, Kalign, MAFFT, MSAProbs, MUSCLE, T-Coffee
  Sequence Analysis: Aln2Plot, DeepCoil, DeepCoil2, HHrepID, MARCOIL, PCOILS, REPPER, TPRpred
  Secondary Structure: Ali2D, HHomp, Quick2D
  Tertiary Stucture: MODELLER, SamCC
  Classification: ANESCON, CLANS, MMseqs2, PhyML
  Utilities: 6FrameTranslation, BackTranslator, FormatSeq, HHfilter, RetrieveSeq, Seq2ID, Reformat

btwisted

• Description : btwisted tool computes the twisting in a B-DNA sequence. The algorithm takes a DNA sequence and uses uncomplicated arithmetic to calculate the sequence twist and its stacking energy.

cgDNA

• Description : cgDNA is a tool to make a DNA molecule in the minimal free energy configuration. The cgDNA algorithm has functions for computing the associated stiffness in the specific energy configuration and comparisons between multiple DNA shapes. The input and output are Curves+ and PDB atom coordinate -formats.

cgDNAweb

• Description : cgDNAweb is a web-based tool to interactively visualize the cgDNA tool predictions of the minimal free energy state of DNA double helices. The cgDNAweb can visualize the ground state configurations as 2D, 3D plots at several levels of detail.

CURVES+

• Description : Curves+ is a web-based tool to analyze and visualize nucleic acid structures, the helical backbone and groove parameters.

dnaMATE

• Description : dnaMATE is a tool to calculate consensus melting and annealing temperatures for short DNA sequences of 16 to 30 nucleotides of length. The dnaMATE uses three independent thermodynamic data tables for the calculations, gives five separate approximations, a consensus temperature, and an expected melting temperature variation estimate. A stand-alone version is available.

J-Circos

• Description : J-Circos is a tool to plot 3-dimensional, circular (Circos) figures for chromosomal interactions. J-Circos lets users zoom, to append data to figures, and show details on mouse hover.

Non-B_DB

• Description : Non-B DB is an online database that contains non-B DNA forming sequence motifs. The Non-B DB includes predictions for Z-DNA, quadruplex-forming motifs, mirror repeats, inverted repeats, and direct repeats with subsets of cruciforms, triplex, and slipped structures.
  The database also contains disease-associated motifs, such as short tandem repeats and homo(purine•pyrimidine) tracts.
  The query results link to the UCSC browser and GBrowse-based genomic viewers.

NUCwave

• Description : NUCwave is a tool to create nucleosome occupation maps from Chromatin digestion with micrococcal nuclease (MNase-seq), Chemical cleavage of chromatin (CC-seq), and Chromatin immunoprecipitation (ChIP-seq) and fragmentation by sonication. The NUCwave algorithm can use both single-read and paired-end sequencing protocols.

OligoCalc

• Description : OligoCalc is a tool to calculate the melting temperature, concentration, molecular weight, absorbance at 260 nanometers, and physical properties of single- and double-stranded DNA and RNA molecules. OligoCalc algorithm recognizes 5’ and 3’ chemical modifications and predicts potential hairpin loops.

Pegasys

• Description : Pegasys is a web-based service containing numerous tools for sequence analyses, such as Agave, Alignment Tools, BRENDA, CpGAT, Edit Tools, Emboss, Information Tools, Kegg Search, Nucleic Tools, Phylogeny Tools, Protein Tools, Sabio - Rk, and Similarity Search Tools.
  
  A user can create custom analysis workflows with the Pegasys system using a graphical interface.

Stitchprofiles

• Description : Stitchprofiles.uio.no is a web-based tool to predict DNA melting. Stitchprofiles.uio.no computes stitch profiles, melting curves, probability profiles, temperature profiles, loop entropies, and plots profile diagrams, visualizes DNA conformations with probabilities.

triplex

• Description : Triplex is an R tool to identify and visualize intramolecular triplex patterns in DNA sequences. The Triplex algorithm detects subsequence positions that can fold into an intramolecular triplex (H-DNA) and visualizes the base-pairing in 1-D, 2-D and 3-D.

ValFold

• Description : ValFold is a tool to predict DNA secondary structures. The ValFold algorithm uses unique aptamer properties and predicts canonical Watson-Crick pairs and G-G pairs from G-quadruplex structures applying the stem candidate selection algorithm.

VarGibbs

• Description : VarGibbs Tool computes nearest-neighbor DNA entropies and initiation parameters from experimental melting temperatures. The VarGibbs algorithm is similar to the Peyrard-Bishop nearest-neighbor model.

wtdbg2

• Description : wtdbg2 is long-read based assembler that is 2 to 17 times faster than some published tools (as of 2020) that performed the same task. The algorithm basically follows the overlap-layout-consensus method but advanced it with a fast all-versus-all read alignment process. It also uses fuzzy-Bruijn graph.

RNA Structure Analysis Tools

4SALE

• Description : 4SALE is a tool for the asynchronous alignment of RNA secondary structures. 4SALE has a graphical interface written in Java, provides synchronous editing of the sequence alignments and secondary structures, and direct access to the ITS2 Database. The features include the ability to select multiple sections of an alignment, highlighting of sequence-motifs by pattern matching, visualization of sequence information using sequence logos or bars, and reordering of sequences.

APTANI

• Description : APTANI is a tool for the identification of aptamers (synthetic nucleic acid molecules that can bind biological targets) from HT-SELEX data and secondary structure information.

Assemble2

• Description : Assemble2 is a tool for designing RNA secondary structures that allows you to assemble the modules in UCSF Chimera. The Assemble2 algorithm includes the following functions: 1. A complete 3-D modeling workflow, 2. Prediction of 2-D structures, 3. Editing 2-D structures, 4. Creation of structural alignments, 5. Guided 3-D modeling, 6. 3-D modeling in Density Maps, 7. A geometric refinement to optimize 3-D structures. Assemble uses Web Services.

BARNACLE

• Description : BARNACLE is a library to predict 3D RNA structures given a nucleotide sequence.

BEAM

• Description : BEAM (BEAr Motifs finder) is a web-based tool to identify and analyze RNA secondary structures. The BEAM algorithm computes the statistical significance of each motif, uses information from the RFAM database of families of homologous RNAs, produces logos and shared positions for each of the motifs. It uses RNAfold (MFE) or RNAstructure (MEA) for folding. The BEAM algorithm transforms RNA secondary structures into character strings to speed up to achieve rapid computation..

CapR

• Description : CapR is a tool for the analysis of RNA secondary structures by computing the probabilities of each RNA base position location within the structural categories of the stem part, hairpin loop, bulge loop, internal loop, multibranch loop, and exterior loop.

CARNA web server

• Description : CARNA is a tool to construct multiple sequence alignments of RNA. The CARNA algorithm computes probability matrices or uses user-provided matrices or user-provided fixed structures, and computes alignments that have the best fit among all potential RNA structures. CARNA can also align random pseudoknots.

CARNAC

• Description : CARNAC is a tool for the analysis and prediction of conserved secondary structures in homologous RNAs. The CARNAC algorithm uses a thermodynamic model to minimize the energies and mutual information in sequences. This way, CARNAC can predict sequences that share a secondary structure without the need for them to be aligned.

catRAPID signature

• Description : catRAPID signature is a web-based tool to calculate RNA-binding binding propensity and specific RNA-binding regions. The catRAPID algorithm uses Physico-chemical features to identify ribonucleoproteins and visualizes the results directly on the web page that are downloadable or forwardable to the catRAPID omics to predict RNA targets. The Authors have trained catRAPID signature on human proteins.

COGNAC

• Description : COGNAC (COnnection tables Graphs for Nucleic ACids) is a web-based tool to search, analyze, and annotate hydrogen-bonded base interactions in 3-dimensional RNA structures. The COGNAC algorithm uses the graph-theoretical implementation of the Ullmann subgraph isomorphism.

cpPredictor

• Description : cpPredictor is a web-based tool to predict the secondary structures of RNAs. The cpPredictor algorithm computes secondary structures given an RNA template structure and a query RNA sequence. cpPredictor also outputs z-scores.

Forna

• Description : forna is a web-based tool to display and edit RNA secondary structures. The visualizations are easily customizable on a web-browser. The forna algorithm uses the d3.js visualization library to visualize force-directed graph layout. You can also install the server locally inot your on computer.

GARN2

• Description : GARN / GARN2 (Game Algorithm for RNa sampling) is a tool to compute RNA 3D structures from a secondary structure. The GARN algorithm uses a regret minimization method.

K2N

• Description : K2N is a tool that provides several different algorithms to remove pseudoknots to make knotted RNA structures to nested structures.

OligoCalc

• Description : OligoCalc is a tool to calculate the melting temperature, concentration, molecular weight, absorbance at 260 nanometers, and physical properties of single- and double-stranded DNA and RNA molecules. OligoCalc algorithm recognizes 5’ and 3’ chemical modifications and predicts potential hairpin loops.

Pegasys

• Description : Pegasys is a web-based service containing numerous tools for sequence analyses, such as Agave, Alignment Tools, BRENDA, CpGAT, Edit Tools, Emboss, Information Tools, Kegg Search, Nucleic Tools, Phylogeny Tools, Protein Tools, Sabio - Rk, and Similarity Search Tools.
  
  A user can create custom analysis workflows with the Pegasys system using a graphical interface.

RiboCAT

• Description : RiboCAT (Ribonucleic acid Capillary-electrophoresis Analysis Tool) is a Microsoft Excel-based tool for the analysis of RNA probing data from capillary electrophoresis. RiboDOG (RiboCAT Data Output Generator) tool formats RiboCAT output error-checking and RNAStructure input files.

RiboVision

• Description : RiboVision is a web-based tool to retrieve, filter, analyze ribosomal data, and visualize ribosome 1-D, 2-D, and 3-D structures. The RiboVision algorithm includes base-pairing, base-stacking, and other molecular interactions data to the structural information. RiboVision has data and structures for Thermus thermophilus, Escherichia coli bacterial ribosomes, Haloarcula marismortui archaeal ribosome, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens eukaryotic ribosomes. RiboVision allows uploading data from CSV files onto 1D, 2D, and 3D structures.

RNAcop

• Description : RNAcop (RNA Context Optimization by Probability) is a tool to optimize lengths of flanking regions up- and downstream of a probable structure fold. The RNAcop algorithm progressively adds nucleotides to flanking regions of a sequence to determine the one having the highest probability of a constrained structure.

RNAparametric

• Description : RNAparametric is a web-based tool to compute the minimum free energy structures of RNA. The RNAparametric package consists of RNAhairpin, RNAmloopNum, RNAmloopOrder, and RNAmloopHP algorithms that compute the Boltzmann partition function for hairpins, the number of multiloops, maximum depth of multiloops, and the concurrent number of hairpins and multiloops. The Boltzmann probabilities of the hairpin and multiloop structures are beneficial as added characteristics in discovering noncoding RNAs.

SETTER

• Description : SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) is a web-based tool to compare RNA secondary structures. The SETTER algorithm uses tertiary structure similarity to produce secondary structure alignments and compute both pair-wise (SETTER) and multiple alignments (MultiSETTER). The MultiSETTER algorithm computes an average structure and superimposes the input structures on to it.

SPuNC

• Description : SPuNC (Structure Prediction using Nucleotide Composition) is a tool to predict RNA structures. The SPuNC algorithm uses evolutionary patterns of nucleotide composition. Note that the code is not maintained anymore.

supernmotifs

• Description : super-n-motifs is a tool to compare secondary linear and circular RNA structures. super-n-motifs algorithm accounts for pseudoknot, G4 motifs, and uses an alignment-free method.

TRAVeLer

• Description : Traveler is a tool to visualize RNA secondary structures. The Traveler algorithm takes a target and a template structure as inputs. It computes tree representations and calculates tree edit distances with layout adjustment operations to transform the template layout into the target layout.

---