Ref: http://bioinformatics.igc.gulbenkian.pt/resources/tools/sequenceanalysis
List of exhaustive tools with links to sequence analysis
- Sequence Manipulation
- Restriction Analysis
- Primer Design
- Finding Genes
- Finding Promoters and Regulatory Elements
- Identify Splice Junctions
- Sequence Repeat Finders
- Sequence Motif Finders
- Translation Tools
- Post-Translational Modifications
- Align Two Sequences
- Multiple Sequence Alignment
- BLAST
tool
|
description
|
Sequence Manipulation Suite - Here you can find a
collection of programs for generating, formatting, and analyzing DNA and
protein sequences.
|
|
Tool from the EMBOSS package joins two overlapping nucleic
acid sequences into one merged sequence.
|
|
Tool to convert a DNA sequence into its reverse,
complement, or reverse-complement .
|
tool
|
description
|
Restriction Enzyme Database - search for restriction
enzymes by name, species, recognition sequence, companies that sell
restriction enzymes or by authors and citations associated with each enzyme.
|
|
A nice site for generating retriction maps and
identification of non-overlapping ORFs.
|
|
Generate several types of graphics and text-based maps for
restriction enzymes.
|
|
An on-line tool for restriction analysis, silent mutation
scanning, and SNP-RFLP analysis.
|
tool
|
description
|
Primer3 is a widely used
program for designing PCR primers.
|
|
Application that accepts a multiple species nucleotide
alignment file as input and identifies a set of PCR primers that will bind
across the alignment. The program iteratively runs the Primer3 application
for each alignment sequence and collates the results.
|
|
Design intron-spanning assays for your target gene. You can
select the organism of interest and enter the target-gene name, gene ID or
nucleotide sequence.
|
|
Real Time PCR primer design.
|
|
The Consensus-degenerate hybrid oligonucleotide primers
program designs PCR primers from protein multiple-sequence alignments and is
intended for cases where the protein sequences are distant from each other
and degenerate primers are needed
Help.
|
|
Method for designing degenerate primers based on multiple
local alignments employing the MEME algorithm supported with electronic PCR.
|
tool
|
description
|
Gene identification program which analyzes genomic DNA
sequences from a variety of organisms including human, other vertebrates,
invertebrates and plants.
|
|
Package of programs for gene prediction in Bacteria,
Archaea and Metagenomes; Eukaryotes; Viruses, Phages and Plasmids and EST.
|
|
Gene finding in Eukaryote, Bacteria and Virus.
|
|
Software that predicts exons, genes, promoters, polyAs, CpG
islands, EST similarities, and repetitive elements within DNA sequence.
|
|
Software that performs gene predictions on microbial and
model organisms and produce a set of data which can be used by GrailEXP v3.0
to recognize genes in these organisms.
|
|
Prediction of gene start location in mammalian genomes, by
combining information about CpG islands, transcription start sites (TSSs),
and signals downstream of the predicted TSSs.
|
|
Software thar compares a protein sequence to a genomic DNA
sequence, allowing for introns and frameshifting errors.
|
|
A list of gene prediction programs for both eukaryotic and
prokaryotic organisms.
|
tool
|
description
|
Searching DNA for eukaryotic transcription Factor Binding
Sites and DNA-binding profiles (searches TransFAC).
|
|
Tool for finding cis-regulatory elements in genomic
sequences. Predictions are based on the integration of binding site
prediction generated with high-quality transcription factor models and
cross-species comparison filtering (phylogenetic footprinting).
|
|
Web tool for predicting transcription factor binding sites
in DNA sequences. It can identify binding sites using site or consensus
strings and positional weight matrices from the TRANSFAC, JASPAR, IMD,
CBIL-GibbsMat database. You can use TESS to search a few of your own sequences
or for user-defined CRMs genome-wide near genes throughout genomes of
interest.
|
|
Gene finding in Eukaryote, Bacteria and Virus. Go to Test on Line on the left
side, and seach on search Motifs
menu.
|
|
Neural Network Promoter Prediction - Promoter Prediction by
Neural Network for prokaryotes or eukaryotes.
|
|
Predicts Promoter regions based on scoring homologies with
putative eukaryotic Pol II promoter sequences.
|
|
Predicts transcription start sites of vertebrate PolII
promoters in DNA sequences.
|
tool
|
description
|
Splice Site Prediction by Neural Network for drosophila and
human/other Help.
|
|
The NetGene2 server is a service producing neural network
predictions of splice sites in human, C. elegans and A. thaliana DNA Help.
|
|
MaxEntScan was used to score the splice site signals of
each exon-intron junction. MaxEntScan is based on the approach for modeling
the sequences of short sequence motifs such as those involved in RNA splicing
which simultaneously accounts for non-adjacent as well as adjacent
dependencies between positions.
|
|
The Splicing RegulatiOn Online Graphical Engine combines:
1)Availability of data - accessibility to large sets of published data; 2)
Integration of data - integrative overview of the signals characterizing
exons of interest; 3) Intuitive statistical measures -many algorithms provide
output which are not directly interpretable (e.g. delta-G scores, PSSM log
odd scores), etc.. 4) User friendliness - intuitive, interactive, graphical
user interface and on dynamic java-script programming, enabling users to
interactively modify their input. Help.
|
|
The Human Splicing Finder is an online bioinformatics tool
to predict the effects of mutations on splicing signals or to identify
splicing motifs in any human sequence. Help.
|
|
SplicePort is a splice-site analysis tool that makes
splice-site predictions for submitted sequences, and allows browsing of
predictive signals and motif exploration. This collection of signals is
capable of achieving high classification accuracy on human splice sites. Help.
|
|
Prediction of putative alternative exon isoform, cryptic,
and constitutive splice sites of internal (coding) exons Help.
|
tool
|
description
|
Program that screens DNA sequences for low complexity DNA
sequences and interspersed repeats. The masked out sequence can be used for
example BLAST searches. Repeats are stored in the datbase Repbase update.
|
tool
|
description
|
Scan Nucleotide or Protein Sequences for Matching Patterns.
|
|
Estimated Locations of Pattern Hits - Find motifs in a set
of DNA or protein sequences Tutorial.
|
tool
|
description
|
Tool from the EMBOSS package, translates nucleic acid
sequences to the corresponding peptide sequence. It has option for which Genetic
Code Table to use.
|
|
This tool allows the translation of a nucleotide (DNA/RNA)
sequence to a protein sequence using the standard genetic code.
|
|
Open Reading Frame Finder is a graphical
analysis tool which finds all open reading frames of a selectable minimum
size in a user’s sequence or in a sequence already in the database using the
standard or alternative genetic codes.
|
tool
|
description
|
Post-translationam modification tutorial.
|
|
A survey of publicly available PTM web resources, databases
and classification/prediction servers.
|
|
Tool that can predict the possible oligosaccharide
structures that occur on proteins from their experimentally determined
masses. The program can be used for free or derivatized oligosaccharides and
for glycopeptides.
|
|
This tool predicts N-terminal myristoylation of proteins by
neural networks.Only N-terminal glycines are myristoylated (leading
methionines are cleaved prior to myristoylation).
|
|
Group-based Phosphorylation Scoring method is a tool for in
silico prediction of phosphorylation sites with their specific kinases.
|
|
Tool that produces neural network predictions for serine,
threonine and tyrosine phosphorylation sites in eukaryotic proteins.
|
|
Tool for in silico sumoylation sites prediction.
SUMOylation, a reversible post-translational modification of proteins by the
small ubiquitin-related modifiers (SUMO), is crucial in a variety of
biological processes.
|
tool
|
description
|
This tool produces the alignment of two given sequences
using the NCBI BLAST engine for local alignment. The output shows the similar
region.
|
|
EMBOSS Pairwise Alignment Algorithms tool used to compare 2
sequences when you want an alignment that covers the whole length of both
sequences.
|
|
EMBOSS Pairwise Alignment Algorithms tool used when you are
trying to find the best region of similarity between two sequences.
|
tool
|
description
|
Multiple sequence alignment for DNA or proteins with
hierarchical clustering.
|
|
Multiple sequence alignment program for DNA or proteins
sequences. It calculates the best match for the selected sequences, and lines
them up so that the identities, similarities and differences can be seen.
Evolutionary relationships can be seen via viewing Cladograms or Phylograms.
|
|
Computes a multiple sequence alignment and the associated
phylogenetic tree for a set of sequences (Proteins or DNA). T-Coffee allows
the combination of a collection of multiple/pairwise, global or local
alignments into a single model. It also allows to estimate the level of
consistency of each position within the new alignment with the rest of the
alignments.
|
tool
| <><>
description
| <><><> <>
|
| <><><> <>
The Basic Local Alignment Search Tool (NCBI) finds regions
of local similarity between sequences. The program compares nucleotide or
protein sequences to sequence databases and calculates the statistical
significance of matches Tutorial.
| <><><> <>
|
| <><><> <>
Here you can find a list of all the Blast´s available at
the EBI including the Ensembl Multi BlastView to the annotated genomes.
|
UCSC Genome Browser Utilities
|
Acknowledged the contribution of the UCSC Genome Bioinformatics
Group.
. Batch Coordinate Conversion (liftOver) -
converts genome coordinates and genome annotation files between assemblies. The
current version supports both forward and reverse conversions, as well as
conversions between selected species.
. DNA Duster
- removes formatting characters and other non-sequence-related characters from
an input sequence. Offers several configuration options for the output format,
including translated protein.
. Protein Duster - removes formatting characters and other non-sequence-related characters from an input sequence. Offers several configuration options for the output format. . Phylogenetic Tree Gif Maker - creates a gif image from the phylogenetic tree specification given. Offers several configuration options for branch lengths, normalized lengths, branch labels, legend etc. . Source Code Downloads - The Genome Browser, Blat and liftOver source code is freely downloadable for academic, noncommercial, and personal use. |
Gene prediction
software
Ab
initio approaches
Name
|
Description
|
Links
|
References
|
identifying translational initiation sites in cDNA
sequences
|
|||
predicts genes in eukaryotic genomic sequences
|
|||
hidden Markov model (HMM) and dynamic programming based ab initio
gene prediction program
|
|||
a system for fast detection of coding regions in short
genomic sequences
|
|||
software for recognition of vertebrate RNA Polymerase II
promoters
|
|||
gene finding for Arabidopsis thaliana
|
|||
find genes and frameshift
in G+C
rich prokaryotic
sequences
|
|||
linking ORFs in complete genomes to protein 3D structures
|
|||
program to predict genes, exons, splice sites and other
signals along a DNA sequence
|
|||
Parse a DNA sequence into introns and exons
|
|||
family of gene prediction programs
|
|||
gene prediction program for prokaryotes and eukaryotes
|
|||
prediction of genes with frameshifts
in prokaryotic genomes
|
|||
web tool for combining results from different programs
(GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH,
REPEATMASKER, TRNASCAN)
|
|||
finding genes in microbial DNA
|
|||
hidden markov model for finding genes in vertebrate DNA
Server
|
|||
a decision tree system for finding genes in vertebrate DNA
|
|||
a method to identify potential splice sites in (plant)
pre-mRNA by sequence inspection using Bayesian statistical models
|
|||
finding genes using Fourier transform
|
|||
promoter prediction by neural network
|
|||
splice site prediction by neural network
|
|||
provides a series of modular computer programs specifically
designed for the detection of regulatory signals in non-coding sequences.
|
|||
predicts locations and exon-intron structures of genes in
genomic sequences from a variety of organisms.
|
|||
a graphical analysis tool which finds all open reading
frames
|
|||
predicts exons, genes, promoters, polyas, CpG islands, EST
similarities, and repetitive elements within DNA sequence
|
RNA structure
prediction software
Single
sequence secondary structure prediction
Name
|
Description
|
Knots
|
Links
|
References
|
|
Secondary structure prediction based on generalized
centroid estimator
|
no
|
||||
Secondary structure prediction by using homologous sequence
information
|
no
|
||||
Secondary structure prediction method based on conditional
log-linear models (CLLMs), a flexible class of probabilistic models which
generalize upon SCFGs
by using discriminative training and feature-rich
scoring.
|
no
|
||||
Secondary structure prediction method based on placement of
helices allowing complex pseudoknots.
|
yes
|
||||
Folding kinetics of RNA sequences including pseudoknots by
including an implementation of the partition function for knots.
|
yes
|
||||
MFE (Minimum Free Energy) RNA structure
prediction algorithm.
|
no
|
||||
A dynamic programming algorithm for optimal RNA pseudoknot
prediction using the nearest neighbour energy model.
|
yes
|
||||
A dynamic programming algorithm for the prediction of a
restricted class of RNA pseudoknots.
|
yes
|
||||
Secondary structure prediction via thermodynamic-based
folding algorithms and novel structure-based sequence alignment specific for
RNA.
|
yes
|
||||
MFE RNA structure prediction algorithm. Includes an
implementation of the partition function for computing basepair probabilities
and circular RNA folding.
|
no
|
[7][10][11][12][13][14] |
|||
MFE RNA structure prediction based on abstract shapes.
Shape abstraction retains adjacency and nesting of structural features, but
disregards helix lengths, thus reduces the number of suboptimal solutions
without losing significant information. Furthermore, shapes represent classes
of structures for which probabilities based on Boltzmann-weighted energies
can be computed.
|
no
|
||||
A program to predict lowest free energy structures and base
pair probabilities for RNA or DNA sequences. Programs are also available to
predict Maximum Expected Accuracy structures and these can include
pseudoknots. Structure prediction can be constrained using experimental data,
including SHAPE, enzymatic cleavage, and chemical modification accessibility.
Graphical user interfaces are available for Windows and for Mac OS-X/Linux.
Programs are also available for use with Unix-style text interfaces.
Additionally, a C++ class library is available.
|
yes
|
[17][18] |
|||
Statistical sampling of all possible structures. The sampling
is weighted by partition function probabilities.
|
no
|
||||
The UNAFold software package is an integrated collection of
programs that simulate folding, hybridization, and melting pathways for one
or two single-stranded nucleic acid sequences.
|
no
|
||||
Crumple is simple, cleanly written software for producing
the full set of possible secondary structures for a single sequence, given
optional constraints.
|
no
|
||||
Sliding windows and assembly is a tool chain for folding
long series of similar hairpins.
|
no
|
Name
|
Description
|
Knots
|
Links
|
References
|
|
A Python library for the probabilistic sampling of RNA
structures that are compatible with a given nucleotide sequence and that are
RNA-like on a local length scale.
|
yes
|
||||
Automated de novo prediction of native-like RNA tertiary
structures .
|
yes
|
||||
three-dimensional RNA structure prediction and folding
|
yes
|
||||
Thermodynamics and Nucleotide cyclic motifs for RNA
structure prediction algorithm. 2D and 3D structures.
|
yes
|
||||
Coarse-grained modeling of large RNA molecules with
knowledge-based potentials and structural filters
|
?
|
||||
An integrated platform for de novo and homology modeling of
RNA 3D structures, where coordinate file input, sequence editing, sequence
alignment, structure prediction and analysis features are all accessed from a
single intuitive graphical user interface.
|
yes
|
||||
*Knots:
Pseudoknot
prediction, <yes|no>.
|
|||||
The single sequence methods mentioned above have a difficult job detecting a small sample of reasonable secondary structures from a large space of possible structures. A good way to reduce the size of the space is to use evolutionary approaches. Structures that have been conserved by evolution are far more likely to be the functional form. The methods below use this approach.
Name
|
Description
|
Number of
sequences
|
Alignment
|
Structure
|
Knots
|
Link
|
References
|
|
Comparative analysis combined with MFE folding.
|
any
|
no
|
yes
|
no
|
||||
Common secondary structure prediction based on generalized
centroid estimator
|
any
|
yes
|
no
|
no
|
||||
Fast and accurate multiple aligner for RNA sequences
|
any
|
yes
|
no
|
no
|
||||
an expectation maximization algorithm using covariance
models for motif description. Uses heuristics for effective motif search, and
a Bayesian framework for structure prediction combining folding energy and
sequence covariation.
|
yes
|
yes
|
no
|
|||||
implements a pinned Sankoff algorithm for simultaneous
pairwise RNA alignment and consensus structure prediction.
|
2
|
yes
|
yes
|
no
|
||||
an algorithm that improves the accuracy of structure
prediction by combining free energy minimization and comparative sequence
analysis to find a low free energy structure common to two sequences without
requiring any sequence identity.
|
2
|
yes
|
yes
|
no
|
||||
A multiple RNA structural RNA alignment method, to a large
extend based on the PMcomp program.
|
any
|
yes
|
yes
|
no
|
||||
Computes a consensus RNA secondary structure from an RNA
sequence alignment based on machine learning.
|
any
|
input
|
yes
|
yes
|
||||
Produce a global fold and alignment of ncRNA families using
integer linear programming and Lagrangian relaxation.
|
any
|
yes
|
yes
|
no
|
||||
LocaRNA is the successor of PMcomp with an improved time
complexity. It is a variant of Sankoff's algorithm for simultaneous folding
and alignment, which takes as input pre-computed base pair probability
matrices from McCaskill's algorithm as produced by RNAfold -p. Thus the
method can also be viewed as way to compare base pair probability matrices.
|
any
|
yes
|
yes
|
no
|
||||
A sampling approach using Markov chain Monte Carlo in a simulated annealing framework, where both
structure and alignment is optimized by making small local changes. The score
combines the log-likelihood of the alignment, a covariation term and the
basepair probabilities.
|
any
|
yes
|
yes
|
no
|
||||
a multiple alignment tool for RNA sequences using iterative
alignment based on Sankoff's algorithm with sharply reduced computational
time and memory.
|
any
|
yes
|
yes
|
no
|
||||
a multiple alignment tool for RNA sequences using
progressive alignment based on pairwise structural alignment algorithm of
SCARNA.
|
any
|
yes
|
yes
|
no
|
||||
A method for joint prediction of alignment and common
secondary structures of two RNA sequences using a probabilistic model based
on pseudo free energies obtained from precomputed base pairing and alignment
probabilities.
|
2
|
yes
|
yes
|
no
|
||||
Folds alignments using a SCFG trained on rRNA alignments.
|
input
|
yes
|
no
|
|||||
Formally integrates both the energy-based and
evolution-based approaches in one model to predict the folding of multiple
aligned RNA sequences by a maximum expected accuracy scoring. The structural
probabilities are calculated by RNAfold and Pfold.
|
any
|
input
|
yes
|
no
|
||||
PMcomp is a variant of Sankoff's algorithm for simultaneous
folding and alignment, which takes as input pre-computed base pair
probability matrices from McCaskill's algorithm as produced by RNAfold -p.
Thus the method can also be viewed as way to compare base pair probability
matrices. PMmulti is a wrapper program that does progressive multiple
alignments by repeatedly calling pmcomp
|
yes
|
yes
|
no
|
|||||
uses RNAlpfold to compute the secondary structure of the
provided sequences. A modified version of T-Coffee is
then used to compute the multiple sequence alignment having the best
agreement with the sequences and the structures. R-Coffee can be combined
with any existing sequence alignment method.
|
any
|
yes
|
yes
|
no
|
||||
The structure based sequence alignment (SBSA) algorithm
within RNA123 utilizes a novel suboptimal version of the Needleman-Wunsch
global sequence alignment method that fully accounts for secondary structure
in the template and query. It also utilizes two separate substitution
matrices that are optimized for RNA helices and single stranded regions. The
SBSA algorithm provides >90% accurate sequence alignments even for
structures as large as bacterial 23S rRNA (~2800 nts).
|
any
|
yes
|
yes
|
yes
|
||||
Folds precomputed alignments using a combination of
free-energy and a covariation measures. Ships with the Vienna package.
|
any
|
input
|
yes
|
no
|
||||
enumerates the near-optimal abstract shape space, and
predicts as the consensus an abstract shape common to all sequences, and for
each sequence, the thermodynamically best structure which has this abstract
shape.
|
any
|
no
|
yes
|
no
|
||||
Compare and align RNA secondary structures via a
"forest alignment" approach.
|
any
|
yes
|
input
|
no
|
||||
Frequent stem pattern miner from unaligned RNA sequences is
a software tool to extract the structural motifs from a set of RNA sequences.
|
any
|
no
|
yes
|
no
|
||||
A probabilistic sampling approach that combines
intrasequence base pairing probabilities with intersequence base alignment
probabilities. This is used to sample possible stems for each sequence and
compare these stems between all pairs of sequences to predict a consensus
structure for two sequences. The method is extended to predict the common
structure conserved among multiple sequences by using a consistency-based
score that incorporates information from all the pairwise structural
alignments.
|
any
|
yes
|
yes
|
yes
|
||||
Stem Candidate Aligner for RNA (Scarna) is a fast,
convenient tool for structural alignment of a pair of RNA sequences. It
aligns two RNA sequences and calculates the similarities of them, based on
the estimated common secondary structures. It works even for pseudoknotted
secondary structures.
|
2
|
yes
|
yes
|
no
|
||||
simultaneously inferring RNA structures including
pseudoknots, alignments, and trees using a Bayesian MCMC framework.
|
any
|
yes
|
yes
|
yes
|
||||
a program for pairwise RNA structural alignment based on
probabilistic models of RNA structure known as Pair stochastic context-free
grammars.
|
any
|
yes
|
yes
|
no
|
||||
an alignment tool designed to provide multiple alignments
of non-coding RNAs following a fast progressive strategy. It combines the
thermodynamic base pairing information derived from RNAfold calculations in
the form of base pairing probability vectors with the information of the
primary sequence.
|
yes
|
no
|
no
|
|||||
A tool for predicting non-coding RNA secondary structures
including pseudoknots. It takes in input an alignment of RNA sequences and
returns the predicted secondary structure(s).It combines criteria of stability,
conservation and covariation in order to search for stems and pseudoknots.
Users can change different parameters values, set (or not) some known stems
(if there are) which are taken into account by the system, choose to get
several possible structures or only one, search for pseudoknots or not, etc.
|
any
|
yes
|
yes
|
yes
|
||||
a webserver that makes it possible to simultaneously use a
number of state of the art methods for performing multiple alignment and
secondary structure prediction for noncoding RNA sequences.
|
yes
|
yes
|
no
|
|||||
a program for analysis of multiple sequence alignments
using phylogenetic grammars,
that may be viewed as a flexible generalization of the "Pfold"
program.
|
any
|
yes
|
yes
|
no
|
||||
* Number
of sequences: <any|num>. * Alignment: predicts an alignment, <input|yes|no>. * Structure:
predicts structure, <input|yes|no>. * Knots: pseudoknot
prediction, <yes|no>.
|
||||||||
Many ncRNAs function by binding to other RNAs. For example, miRNAs regulate protein coding gene expression by binding to 3' UTRs, small nucleolar RNAs guide post-transcriptional modifications by binding to rRNA, U4 spliceosomal RNA and U6 spliceosomal RNA bind to each other forming part of the spliceosome and many small bacterial RNAs regulate gene expression by antisense interactions E.g. GcvB, OxyS and RyhB.
Name
|
Description
|
Intra-molecular
structure
|
Comparative
|
Link
|
References
|
GUUGle
|
A utility for fast determination of RNA-RNA matches with
perfect hybridization via A-U, C-G, and G-U base pairing.
|
no
|
no
|
||
IntaRNA
|
Efficient target prediction incorporating the accessibility
of target sites
|
yes
|
no
|
||
Computes the full unpseudoknotted partition function of
interacting strands in dilute solution. Calculates the concentrations, mfes,
and base-pairing probabilities of the ordered complexes below a certain
complexity. Also computes the partition function and basepairing of single
strands including a class of pseudoknotted structures. Also enables design of
ordered complexes.
|
yes
|
no
|
|||
Predicts bimolecular secondary structures with and without
intramolecular structure. Also predicts the hybridization affinity of a short
nucleic acid to an RNA target.
|
yes
|
no
|
|||
calculates the partition function and thermodynamics of
RNA-RNA interactions. It considers all possible joint secondary structure of
two interacting nucleic acids that do not contain pseudoknots, interaction
pseudoknots, or zigzags.
|
yes
|
no
|
|||
Based upon RNAduplex with bonuses for covarying sites
|
no
|
yes
|
|||
works much like RNAfold, but allows to specify two RNA
sequences which are then allowed to form a dimer structure.
|
yes
|
no
|
|||
computes optimal and suboptimal secondary structures for
hybridization. The calculation is simplified by allowing only inter-molecular
base pairs.
|
no
|
no
|
|||
a tool for finding the minimum free energy hybridisation of
a long and a short RNA.
|
no
|
no
|
|||
calculates the thermodynamics of RNA-RNA interactions.
RNA-RNA binding is decomposed into two stages. (1) First the probability that
a sequence interval (e.g. a binding site) remains unpaired is computed. (2)
Then the binding energy given that the binding site is unpaired is calculated
as the optimum over all possible types of bindings.
|
yes
|
no
|
|||
*
|
|||||
MicroRNAs regulate protein coding gene expression by binding to 3' UTRs, there are tools specifically designed for predicting these interactions. For an evaluation of target prediction methods on high-throughput experimental data see (Selbach et al., Nature 2008) [78] and (Alexiou et al., Bioinformatics 2009)[79]
Name
|
Description
|
Species
Specific
|
Intra-molecular
structure
|
Comparative
|
Link
|
References
|
DIANA-microT 3.0 is an algorithm based on several
parameters calculated individually for each microRNA and it combines
conserved and non-conserved microRNA recognition elements into a final
prediction score.
|
human, mouse
|
no
|
yes
|
|||
An animal miRNA target prediction tool based on
miRNA-target complementarity and thermodynamic data.
|
no
|
no
|
no
|
|||
microRNA target gene prediction using a support vector
machine.
|
no
|
no
|
no
|
|||
Combinatorial microRNA target predictions.
|
8 vertebrates
|
no
|
yes
|
|||
Incorporates the role of target-site accessibility, as
determined by base-pairing interactions within the mRNA, in microRNA target
recognition.
|
no
|
yes
|
no
|
|||
The first link (predictions) provides RNA22 predictions for
all protein coding transcripts in human, mouse, roundworm, and fruit fly. It
allows you to visualize the predictions within a cDNA map and also find
transcripts where multiple miR's of interest target. The second web-site link
(custom) first finds putative microRNA binding sites in the sequence of
interest, then identifies the targeted microRNA.
|
no
|
no
|
no
|
|||
a tool for finding the minimum free energy hybridisation of
a long and a short RNA.
|
no
|
no
|
no
|
|||
Sylamer is a method for finding significantly over or
under-represented words in sequences according to a sorted gene list.
Typically it is used to find significant enrichment or depletion of microRNA
or siRNA seed sequences from microarray expression data.
|
no
|
no
|
no
|
|||
TAREF stands for TARget REFiner. It predicts microRNA
targets on the basis of multiple feature information derived from the
flanking regions of the predicted target sites where traditional structure
prediction approach may not be successful to assess the openness. It also
provides an option to use encoded pattern to refine filtering.
|
Yes
|
no
|
no
|
|||
p-TAREF stands for plant TARget REFiner. It identifies
plant microRNA targets on the basis of multiple feature information derived
from the flanking regions of the predicted target sites where traditional
structure prediction approach may not be successful to assess the openness.
It also provides an option to use encoded pattern to refine filtering. It
first time employed power of machine learning approach with scoring scheme
through Support Vector Regression(SVR) while considering structural and
alignment aspects of targeting in plants with plant specific models. p-TAREF
has been implemented in concurrent architecture in server as well as
standalone form, making it one of the very few available target
identification tools able to run concurrently on simple desktops while performing
huge transcriptome level analysis accurately and fast. Besides this, it also
provides an option to experimentally validate the predicted targets, on the
spot, using expression data, which has been integrated in its back-end, to
draw confidence on prediction along with SVR score.p-TAREF performance
benchmarking has been done extensively through different tests and compared
with other plant miRNA target identification tools. p-TAREF was found better
performing.
|
Yes
|
no
|
no
|
|||
Predicts biological targets of miRNAs by searching for the
presence of conserved 8mer and 7mer sites that match the seed region of each
miRNA. Predictions are ranked using site number, site type, and site context,
which includes factors that influence target-site accessibility.
|
vertebrates, flies, nematodes
|
evaluated indirectly
|
yes
|
|||
*
|
||||||
Name
|
Description
|
Number of
sequences
|
Alignment
|
Structure
|
Link
|
References
|
Assessing a multiple sequence alignment for the existence
of an unusual stable and conserved RNA secondary structure.
|
any
|
input
|
yes
|
|||
a comparative method for identifying functional RNA
structures in multiple-sequence alignments. It is based on a probabilistic
model-construction called a phylo-SCFG and exploits the characteristic
differences of the substitution process in stem-pairing and unpaired regions
to make its predictions.
|
any
|
input
|
yes
|
|||
heuristic search for statistically significant conservation
of RNA secondary structure in deep multiple sequence alignments.
|
any
|
input
|
yes
|
|||
This is the code from Elena Rivas that accompanies a
submitted manuscript "Noncoding RNA gene detection using camparative
sequence analysis". QRNA uses comparative genome sequence analysis to
detect conserved RNA secondary structures, including both ncRNA genes and
cis-regulatory RNA structures.
|
2
|
input
|
yes
|
|||
program for predicting structurally conserved and
thermodynamic stable RNA secondary structures in multiple sequence
alignments. It can be used in genome wide screens to detect functional RNA
structures, as found in noncoding RNAs and cis-acting regulatory elements of
mRNAs.
|
any
|
input
|
yes
|
|||
a program for analysis of multiple sequence alignments
using phylogenetic grammars,
that may be viewed as a flexible generalization of the "Evofold"
program.
|
any
|
yes
|
yes
|
|||
Family
specific gene prediction software
Name
|
Description
|
Family
|
Link
|
References
|
ARAGORN
|
ARAGORN detects tRNA and tmRNA in nucleotide sequences.
|
|||
Given a search query, candidate homologs are identified
using BLAST search and then tested for their known miRNA properties, such as
secondary structure, energy, alignment and conservation, in order to assess
their fidelity.
|
||||
RISCbinder
|
Prediction of guide strand of microRNAs.
|
|||
A SVM-based approach that, in conjunction with a
non-stringent filter for consensus secondary structures, is capable of
recognizing microRNA precursors in multiple sequence alignments.
|
||||
RNAmmer
|
||||
Uses a combination of RNA secondary structure prediction
and machine learning that is designed to recognize the two major classes of
snoRNAs, box C/D and box H/ACA snoRNAs, among ncRNA candidate sequences.
|
||||
Search for C/D box methylation guide snoRNA genes in a
genomic sequence.
|
||||
snoSeeker includes two snoRNA-searching programs, CDseeker
and ACAseeker, specific to the detection of C/D snoRNAs and H/ACA
snoRNAs, respectively. snoSeeker has been used to scan four human–mammal
whole-genome alignment (WGA) sequences and identified 54 novel candidates
including 26 orphan candidates as well as 266 known snoRNA genes.
|
||||
a program for the detection of transfer RNA genes in
genomic sequence.
|
||||
.
|
||||
Name
|
Description
|
Link
|
References
|
"Easy RNA Profile IdentificatioN" is an RNA
motif search program reads a sequence alignement and secondary structure, and
automatically infers a statistical "secondary structure profile"
(SSP). An original Dynamic Programming algorithm then matches this SSP onto
any target database, finding solutions and their associated scores.
|
|||
"INFERence of RNA ALignment" is for searching
DNA sequence databases for RNA structure and sequence similarities. It is an
implementation of a special case of profile stochastic context-free grammars
called covariance models (CMs).
|
|||
"pair hidden Markov models on tree structures"
is an extension of pair hidden Markov models defined on alignments of trees.
|
|||
A slow and rigorous or fast and heuristic sequence-based
filter for covariance models.
|
|||
Takes a single RNA sequence with its secondary structure
and utilizes a local alignment algorithm to search a database for homologous
RNAs.
|
|||
.
|
|||
Name
| <><>
Description
| <><>
Structure
| <><>
Alignment
| <><>
Phylogeny
| <><>
Links
| <><>
References
| <><>
| <><> |
A comprehensive comparison of comparative RNA structure
prediction approaches
| <><>
yes
| <><>
no
| <><>
no
| <><>
<><> | <><> |
BRalibase II
| <><>
A benchmark of multiple sequence alignment programs upon
structural RNAs
| <><>
no
| <><>
yes
| <><>
no
| <><>
<><> | <><> |
BRalibase 2.1
| <><>
A benchmark of multiple sequence alignment programs upon
structural RNAs
| <><>
no
| <><>
yes
| <><>
no
| <><>
<><> | <><> |
BRalibase III
| <><>
A critical assessment of the performance of homology
search methods on noncoding RNA
| <><>
no
| <><>
yes
| <><>
no
| <><>
<><> | <><> |
CompaRNA
| <><>
An independent comparison of single-sequence RNA secondary
structure prediction programs
|
yes
|
no
|
no
|
||
Alignment
viewers/editors
Name
|
Description
|
Alignment
|
Structure
|
Link
|
References
|
|
A tool for Synchronous RNA Sequence and Secondary
Structure Alignment and Editing
|
yes
|
yes
|
||||
Colorstock, a command-line script using ANSI terminal
color; SScolor, a Perl script that generates static HTML pages; and Raton, an
AJAX web application generating dynamic HTML. Each tool can be used to color
RNA alignments by secondary structure and to visually highlight compensatory
mutations in stems.
|
yes
|
yes
|
||||
a multiple alignment viewer written in Java.
|
yes
|
no
|
||||
a multiple alignment editor written in Java.
|
yes
|
no
|
||||
a major mode for the Emacs text editor.
It provides functionality to aid the viewing and editing of multiple sequence
alignments of structured RNAs.
|
yes
|
yes
|
||||
A graphical sequence editor for working with structural
alignments of RNA.
|
yes
|
yes
|
||||
Inverse
Folding/RNA design
Name
|
Description
|
Link
|
References
|
An RNA folding game that challenges players to come up
with sequences that fold into a target RNA structure. The best sequences for
a given puzzle are synthesized and their structures are probed through
chemical mapping. The sequences are then scored by the data's agreement to
the target structure and feedback is provided to the players.
|
--
|
||
Although NUPACK can be used to get useful statistics and
properties of an RNA's structure as mentioned above, it's main goal is design
of new sequences that fold into a desired structure.
|
|||
The ViennaRNA package provides RNAInverse, an algorithm
for designing sequences with desired structure.
|
Secondary
structure viewers/editors
Name
|
Description
|
Link
|
References
|
PseudoViewer
|
Automatically visualizing RNA pseudoknot structures as
planar graphs.
|
||
RNA Movies
|
browse sequential paths through RNA secondary structure
landscapes
|
||
RNA2D3D
|
a program for generating, viewing, and comparing
3-dimensional models of RNA
|
||
RNAView/RnamlView
|
Use RNAView to automatically identify and classify the
types of base pairs that are formed in nucleic acid structures. Use RnamlView
to arrange RNA structures.
|
||
VARNA
|
a tool for the automated drawing, visualization and
annotation of the secondary structure of RNA, designed as a companion
software for web servers and databases
|
A list of
computer programs that are used for nucleic
acids simulations
Min - Optimization, MD - Molecular dynamics, MC - Monte Carlo, REM - Replica exchange method,
Crt - Cartesian coordinates. Int - Internal coordinates Exp - Explicit water. Imp - Implicit water.
Lig - Ligands interactions. HA - Hardware accelerated.
Name
|
View
3D
|
Model
Build
|
Min
|
MD
|
MC
|
REM
|
Crt
|
Int
|
Exp
|
Imp
|
Lig
|
HA
|
Comments
|
License
|
Homepage
|
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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Free
|
||||
| + |
+
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+
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+
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+
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+
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+
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+
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Commercial
|
|||||||
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
|
CHARMM Force Field
|
Commercial
|
||||||
+
|
+
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+
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+
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+
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+
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Commercial
|
|||||||||
+
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+
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+
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+
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Commercial
|
|||||||||||
+
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+
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+
|
+
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+
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+
|
Common MD
|
|||||||||
+
|
+
|
+
|
+
|
+
|
+
|
+
|
Molecular Operating Environment
|
Commercial
|
|||||||
+
|
Nucleic Acid Builder
|
||||||||||||||
+
|
+
|
+
|
+
|
+
|
+
|
+
|
NAnoscale Molecular Dynamics
|
Free
|
