BLESS / BLoom-filter-based Error correction Solution for high-throughput Sequencing reads
Corrects errors related to Bloom filter for high-throughput sequencing reads. BLESS employs the quality score distribution of input reads to fix errors in solid k-mers, k-mers that exist multiple times in reads. It also uses a histogram to determine the threshold for solid k-mers. It is also useful for investigating quality scores or counting k-mers using k-mer counter (KMC).
JEPETTO
Performs integrated gene set analysis using information from interaction, pathways and processes databases. JEPETTO uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes.
ngsTools
Provides several tools for population genetics analysis from next-generation sequencing (NGS) data. ngsTools includes different methods that deals with low-depth sequencing datasets with multiple individuals and populations and can combine deviations from Hardy-Weinberg equilibrium. This software furnishes other functions such as performing population genetics analyses from sample allele frequency posterior probabilities or estimation of individual inbreeding coefficients from genotype likelihoods.
Cascade
Temporal gene interactions, in response to environmental stress, form a complex system that can be efficiently described using gene regulatory networks. They allow highlighting the more influential genes and spotting some targets for biological intervention experiments. Despite that many reverse engineering tools have been designed, the Cascade package is an integrated solution adding several new and original key features such as the ability to predict changes in gene expressions after a biological perturbation in the network and graphical outputs that allow monitoring the spread of a signal through the network.
AltAnalyze
An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).
GraphProt
It can be used for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.
RNAcontext
A motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures.
PIPE-CLIP
A web tool which provides a pipeline for both bioinformaticians and biologist to identify the most likely cross-linking sites from PAR-CLIP, HITS-CLIP and iCLIP sequencing data.
wavClusteR
A statistical and computational framework for PAR-CLIP data analysis. A sensitive transition-centered algorithm specifically designed to resolve protein binding sites at high resolution in PAR-CLIP data was developed. This method employes a Bayesian network approach to associate posterior log-odds with the observed transitions, providing an overall quantification of the confidence in RNA-protein interaction.
MutPred Splice
A machine-learning approach for the identification of coding region substitutions that disrupt pre-mRNA splicing. Applying MutPred Splice to human disease-causing exonic mutations suggests that 16% of mutations causing inherited disease and 10 to 14% of somatic mutations in cancer may disrupt pre-mRNA splicing.
SKIPPY
A tool for the detection of exonic variants that modulate splicing. SKIPPY allows users to input a set of exonic variants to score them for a number of features (such as changes in splicing regulatory elements) that have been shown to be predictive of known genome variations that cause exon skipping or activation of ectopic splice sites. In this way, variants can be either prioritized for further splicing-based functional analysis or the results can be used as further genomic evidence in cases in which the causative variant is already known.
Spliceman
Predicts how likely distant mutations around annotated splice sites were to disrupt splicing. Spliceman takes a set of DNA sequences with point mutations and returns a ranked list to predict the effects of point mutations on pre-mRNA splicing. The current implementation included the analyses of 11 genomes: human, chimp, rhesus, mouse, rat, dog, cat, chicken, guinea pig, frog and zebrafish.
KGGSeq
A three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing studies. This efficient and comprehensive framework successfully narrowed down whole exome variants to very small numbers of candidate variants in the proof-of-concept examples. The proposed framework will play a very useful role in exome sequencing-based discovery of human Mendelian disease genes.
VariantMaster
Extracts causative variants in familial and sporadic genetic diseases. VariantMaster implements a methodology to evaluate the status (presence or absence) of a variant in familial or case-control contexts. The software allows users to identify causative variants in familial, sporadic germline, and somatic genetic disorders, including cancers. It also allows for the search of causative variants in one or more recurrently mutated genes in a pool of unrelated individuals sharing the same phenotype.
G-BLASTN
A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
FuncAssociate
A web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment.
AmiGO
Provides a set of tools for searching and browsing the Gene Ontology (GO) database. AMIGO visualizes speciation, duplication and horizontal gene transfer events, sequence alignments and descriptive data and external links for both proteins and annotations. The workflow annotation is a two-step process: (i) curators create a model of evolution that is consistent with the observed experimental annotations of modern-day sequences. Once constructed, this model is used in a (ii) step to create inferred annotations over the entire tree. This search box was designed to involve strict selection of terms, which results in coherent annotations within proteins families, as well as across families implicated in a single process.
RamiGO
An R interface to AmiGO that enables visualization of Gene Ontology (GO) trees. Given a list of GO terms, RamiGO uses the AmiGO visualize API to import Graphviz-DOT format files into R, and export these either as images (SVG, PNG) or into Cytoscape for extended network analyses. RamiGO provides easy customization of annotation, highlighting of specific GO terms, colouring of terms by P-value or export of a simplified summary GO tree.
GOProfiler
Provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided.
GOSlimViewer
It is used to provide a high level summary of functions for a dataset. The output can be charted in Excel to obtain publication quality figures. Note that records without annotation are not analyzed by GOSlimViewer.
GOblet
Allows gene and genome annotations. GOblet integrates views delivered by ontologies and metabolic or signaling pathways. It can take into account system-level interactions of cellular components. This tool was used for the detection and integrative study of novel genes specifically expressed and developmentally regulated in murine spermatogenic cells. It is useful for high-throughput processing on user’s local machines.
GoFish
This program allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes.
OnEX / Ontology Evolution Explorer
A system for exploring ontology changes. Currently, OnEX provides access to about 520 versions of 16 well-known life science ontologies. The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application. Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.
OntoVisT
This application is designed for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor.
QuickGO
A web-based tool for browsing the GO and all associated GO annotations provided by the GOA group. QuickGO has implemented in JavaScript, Ajax and HTML, with all major browsers supported.
STRAP / Software Tool for Rapid Annotation of Proteins
The program automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques.
GO / The Gene Ontology Resource
A community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the Gene Ontology (GO) Consortium (GOC) has implemented several processes to increase the quantity, quality and specificity of GO annotations.
GSEA / Gene Set Enrichment Analysis
Evaluates microarray data at the level of gene sets. GSEA aims to determine whether members of a gene set S tend to occur toward the top (or bottom) of the list L, in which case the gene set is correlated with the phenotypic class distinction. This method eases the interpretation of a largescale experiment by identifying pathways and processes, and can boost the signal-to-noise ratio when the members of a gene set exhibit strong cross-correlation, allowing to detect modest changes in individual genes.
GoMapMan
An open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.
PiNGO
A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO.
GOrilla / Gene Ontology enRIchment anaLysis and visuaLizAtion tool
A web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression).
REViGO
A web server that can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds.
mirWIP
Target prediction for animal microRNAs (miRNAs) has been hindered by the small number of verified targets available to evaluate the accuracy of predicted miRNA-target interactions. mirWIP can be used to capture all known conserved miRNA-mRNA target relationships in Caenorhabditis elegans at a lower false-positive rate than can the current standard methods.
LMAT / Livermore Metagenomics Analysis Toolkit
A method presented to shift computational costs to an offline computation by creating a taxonomy/genome index that supports scalable metagenomic classification. LMAT is designed to efficiently assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick 'single pass' analysis of every read allows to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.
MetaPhlAn / Metagenomic Phylogenetic Analysis
Estimates the relative abundance of microbial cells by mapping reads against a reduced set of clade-specific marker sequences. MetaPhlAn accurately profiles microbial communities and requires only minutes to process millions of metagenomic reads. This classifier compares each metagenomic read from a sample to this marker catalog to identify high-confidence matches. It finally compares metagenomic reads against this precomputed marker catalog using nucleotide BLAST searches in order to provide clade abundances for one or more sequenced metagenomes.
RNAmotifs
Recognizes clusters of motifs underlying regulatory principles of alternative splicing and alternative polyadenylation. RNAmotifs computes an enrichment score (ES) on the super-imposed sequences of all the features. It finds possible short motifs, convolutes their signals with a short sliding window.
PRISM / Pair Read Informed Split Mapper
A method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses a split-alignment approach informed by the mapping of paired-end reads, hence enabling breakpoint identification of multiple SV types, including arbitrary-sized inversions, deletions and tandem duplications.
MATCHCLIP
A method that identifies the breakpoints of a CNV using both the positions and CIGAR strings of the reads that cover breakpoints of a CNV. In case the two break points of a CNV are in repeated regions and the break points are not unique, MATCHCLIPS reports the range where the break points can slide.
Mercury
Generates annotated personal genome suitable for further analysis and clinical interpretation. Mercury is an extensible workflow which comprises a library of multiple sequence analysis components including variant calling and annotation as well as a set of validation tools, with the aim of encompassing the complete field of the next generation sequencing (NGS) data analysis. Additionally, this software provides a cloud-based implementation to make information sharable between multiple users.
geneCommittee
A web-based interactive tool for routinely evaluating the discriminative classification power of custom hypothesis in the form of biologically relevant gene sets.
[email protected] / MicroArray Classification BEnchmarking Tool on Host server
Performs microarray classification by providing prediction classification methods using randomizations of the benchmarking dataset. [email protected] offers two services: benchmarking and prediction. Benchmarking, the main service, involves selection and training of an optimal model based on the submitted benchmarking dataset and corresponding class labels. This model is then stored for immediate or later use on prospective data. By using the prediction service, [email protected] offers a way for later evaluation of prospective data by reusing an existing optimal prediction model. This tool was designed for the classification of patient samples, supposing microarray data are represented by an expression matrix characterized by high dimensionality in the sense of a small number of patients and a large number of gene expression levels for each patient.
FiGS / Filter-based Gene Selection
A web-based workbench where user can conveniently compare the classification performances of many different filter-based gene selection procedures.
SET / Signature Evaluation Tool
Allows researchers to evaluate gene signatures based on expression datasets. SET provides a gene filtration threshold for gene identification between biological/clinical analyses and typical feature selection tools. The software supplies a signature evaluation platform that can adapt signatures from a variety of sources including third party analyses or candidates of interest that are deduced by biological knowledge. It can be useful for various evaluations in clinical research.
MF-GE / Multiple Filters enhanced Genetic Ensemble system
A hybrid system for feature selection and sample classification of high-dimensional dataset.
GISTIC / Genomic Identification of Significant Targets in Cancer
Recognizes likely driver somatic copy-number alterations (SCNAs). GISTIC evaluates the frequency and amplitude of observed events. It can be adapted to other copy-number analysis workflows. This tool can integrate other software estimating and segmenting copy-number values from sequencing coverage data. It has been tested on multiple cancer types, including glioblastoma, lung adenocarcinoma, melanoma or colorectal carcinoma.
JISTIC
A tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer.
NGSANE / Next Generation Sequencing Analysis for Enterprises
Builds pipelines for next-generation data processing. NGSANE offers a framework allowing the analysis of data from different experimental protocols. It permits end users and developers to elaborate pipelines from call statements that can be tested on the command line directly without syntax alterations or wrapper script involvement. This application can also be used through the Amazon Elastic Compute Cloud.
Snakemake
Provides an execution environment with a clean and readable specification language to reduce the complexity of creating workflows. Snakemake is a workflow engine inspired by the build system GNU Make. The software interoperates with any installed tool or available web service with well-defined input and output (file) formats. Apart from running on single machines, Snakemake contains a generic mechanism that allows the execution of jobs on a batch system or a compute cluster engine.
Nestly
Facilitates running tools with nested combinations of parameters and inputs. Nestly can set up a comparison of two implementations of an algorithm to prune leaves from a phylogenetic tree to reduce an objective function. This software contains several functions to ease running software. It proceeds by taking a fixed set of parameters and produces a single type of output for every defined combination.
Bpipe
Allows definition and execution of bioinformatics pipelines. Bpipe was created in response to a need to frequently run many variations of a pipeline with stages deleted, inserted, reordered or adjusted. The software is implemented in, a language that supports creation of Domain-Specific Languages for the Java Virtual Machine, and it does not require knowledge of either language to implement pipelines. It includes features such as automatic connection of stages, audit trail or transactional management of tasks.
Parseq
Reconstructs transcription landscape from RNA-Seq read counts. Parseq is a statistical approach for analyzing the RNA-Seq read count profiles along the genome. The software estimates the model parameters, reconstructs local transcription levels, calls transcribed regions and identifies coverage breakpoints based on this framework.
SWAN / Subset-quantile Within Array Normalization
A within array normalization method that substantially reduces the technical variability between the probe types whilst maintaining the important biological differences. The SWAN method makes the assumption that the number of CpGs within the 50 bp probe sequence reflects the underlying biology of the region being interrogated. Hence, the overall distribution of intensities of probes with the same number of CpGs in the probe body should be the same. The method then uses a subset quantile normalization approach to adjust the intensities of the probes on the arrays.
BMIQ
Beta Mixture Quantile Method for normalisation of Illumina Infinium 450k data.
NIMBL / Numerical Identification of Methylation Biomarker Lists
MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.
genomation
Allows annotation, bulk summarization, and visualization of genomic intervals over predefined genomic annotations. Genomation is an R package designed for interrogating diverse types of genomic intervals with or without scores. The software reduces the time needed for data processing and biological inference by providing several functions. It can be used with a variety of genomic interval file types.
NanoStriDE / NanoString Differential Expression
Allows biologists to take raw data produced by a NanoString nCounter analysis system and easily interpret differential expression analysis of this data represented through a heatmap.
NanoStringNorm
A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis. By standardizing code and automating error capture, NanoStringNorm will enable more reproducible and robust analysis of NanoString datasets.
nSolver Analysis Software
A data analysis program that offers nCounter users the ability to quickly and easily QC, normalize, and analyze their data without having to purchase additional software packages.
NAPPA
An algorithm for the pre-processing of mRNA data from the NanoString nCounter software, working from the output RCC files saved as a tab delimited text file and imported into R. NAPPA has been optimised to generate high quality robust data for subsequent analyses by optimizing steps to reduce bias and variability and reducing arbitrary decisions. The NAPPA function also provides options for how each algorithmic step is performed.
miRprimer
Designs primers for polymerase chain reaction (PCR) amplification of microRNAs. miRprimer generates a number of putative primers based on an interpretation of the guidelines for manual primer design into computer language. The availability of automated primer design makes this method an even more attractive option for quantification of microRNA expression. Primers designed with this algorithm were tested in different experiments and have the same success rate as manually designed primers.
ddCt / Delta-Delta-Ct
The ddCt Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.
EasyqpcR
A package based on the qBase algorithms. EasyqpcR allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors. It has been created for low-throughput qPCR data analysis.
HTqPCR
A package for the R statistical computing environment, to enable the processing and analysis of qPCR data across multiple conditions and replicates. HTqPCR performs quality assessment, normalization, data visualization and statistical significance testing for Ct values between features (genes and microRNAs) across multiple biological conditions, such as different cell culture treatments, comparative expression profiles or time-series experiments. As it is R based, HTqPCR runs on different operating systems and is easy to incorporate into an analysis pipeline, or used in conjunction with other tools available through the Bioconductor project.
NormqPCR
Provides tools for uploading RT-qPCR data into R, looks for the optimal reference genes, and normalises the data using the ΔΔCq method. NormqPCR allows the user to read RT-qPCR data into R, to deal with undetermined Cq values, to find a suitable reference gene or genes for a given experiment using a method for optimal reference gene selection and to normalise the data via the ΔCq and 2−ΔΔCqnormalisation methods. The user can also use a number of existing bioconductor packages and functions to perform quality control on their data, and can check the adequacy of reference genes visually. Implementing popular optimal reference gene finding algorithms as NormqPCR in the widely-used statistical software for genomic analysis, R, represents an important contribution to the RT-qPCR community, and increases the available options for the analysis of this type of data.
geNorm
An algorithm to determine the most stable reference (housekeeping) genes from a set of tested candidate reference genes in a given sample panel.
NormFinder
It ranks the set of candidate normalization genes according to their expression stability in a given sample set and given experimental design.
BestKeeper
Determines the most appropriate standards and combines them into an index. BestKeeper is an Excel based tool using pair-wise correlations. This application is able to compare expression levels of up to ten housekeeping genes (HKG) together with ten target genes (TG), each in up to hundred biological samples. All data processing operations are based on crossing points.
RefGenes
An online app from Genevestigator that allows users to search for genes that are most stable across a chosen set of samples based on microarray data. This set of samples can be chosen according to experimental conditions or tissue types. For example, if you are performing a RT-qPCR experiment on mouse liver samples, you can use RefGenes to identify the set of genes that are most stable across all microarrays done on mouse liver in Genevestigator.
qbase+
User-friendly software tool for qPCR data analysis. It's based on the qBase and geNorm technologies and is fully MIQE-compliant. Whatever qPCR instrument or computer operating system, whatever type of data or experiment, qbase+ offers an open and flexible solution.
RefFinder
Evaluates and selects reference genes from extensive experimental datasets. RefFinder exploits computational programs (such as BestKeeper, geNorm, Normfinder or the comparative delta-ct method) to rank and compare candidate reference genes. This software measures the geometric mean of the attributed weights for the overall final ranking.
Primer3
Open-source software used for primer design, often in high-throughput genomics applications.
pyQPCR
A GUI application written in python that deals with quantitative PCR (QPCR) raw data.
Primer Designer
This is a program to aid in designing of primers and creation of primer sheets.
PrimerSeq
Designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data.
Amplicon
A tool for designing PCR primers where groups of related DNA sequences can be assessed in aligned form.
JCVI Primer Designer
A fully integrated computational PCR primer design pipeline that plays a key role in high-throughput directed sequencing pipeline.
ORFprimer
A package for automatical primer design. Protein sequences are typically downloaded by simply specifying the GI identifier or accession number of the corresponding protein target. ORFprimer extracts the open reading frame from the requested protein sequences, displays it and automatically calculates PCR primers for these sequences.
Gemi
Fast, automated and user-friendly tool to design polymerase chain reaction (PCR) primers.
AutoPrime
Allows to rapidly design primers for real-time PCR measurement of eucaryotic expression.
BOSS / Batch Oligo Selection Script
A batch primer selection program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps.
SaskPrimerFS
Designed to infer intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.
FastPCR
Predicts primer location and polymerase chain reaction (PCR) product sequences from chromosome lists, whole genomes or circular DNA. FastPCR is an integrated tool that finds all possible primer pairs for conventional or multiplex PCR taking into account mismatches located within the specified primer or target sequence. It performs advanced searching for two or more sequences linked to each other and located within a certain distance.
DPPrimer / Degenerate PCR Primer
It was designed to predict primers for PCR amplification of homologous gene from related or diverse plant species.
HYDEN / HighlY DEgeNerate primers
A program for designing pairs of degenerate primers for a given set of DNA sequences. We report on the success of the program in an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 10(10) that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.
CODEHOP / COnsensus-DEgenerate Hybrid Oligonucleotide Primers
Designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments. CODEHOP is suited for cases where the protein sequences are distant from each other and degenerate primers are needed. Isolation of members of a rapidly evolving family of novel cytosine methyltransferase homologs from diverse plants demonstrated his practical utility.
FAS-DPD / Family-Specific Degenerate Primer Design
A package to design degenerate primers for PCR. FAS-DPD is very strict in the search of conserved regions and minimizes the amount of degeneracy incorporated at this end. The software is designed to use multiple alignments of proteins or nucleic acids and constructs a consensus degenerate sequence from that, which is then used to design the putative primers. This tool allows a more efficient search for enzymes and other proteins with commercial or biotechnological importance, making for a faster and cheaper research process.
GeneFisher2
Allows to design degenerate primers. GeneFisher2 is a web-based program that helps user to find primers for degenerated sequences. The software incorporates BatCons2 which allows to calculate ambiguous consensus sequence and Back-translation of amino-acid to nucleic-acid-sequences. The software provides four functions: Consensus Backtranslation, Codon Table Backtranslation, DNA and Primer Calculation.
dprimer
A command line utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.
Primer-BLAST
Helps users design target-specific primers. Primer-BLAST is a web application that offers flexibility to accommodate different primer design. It incorporates a global alignment mechanism and is designed to be very sensitive in detecting potential amplification targets. Users can either design new primers or check the specificity of pre-existing primers. Finally, it has the capability to place primers based on exon/intron boundaries and Single-Nucleotide Polymorphism (SNP) locations.
In-Silico PCR
Searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance.
e-PCR / Electronic PCR
Identifies sequence tagged sites (STSs) within DNA sequences. e-PCR is a web application which searches for sub-sequences that closely match the polymerase chain reaction (PCR) primers and have the correct order, orientation, and spacing. The software uses overlapping discontinuous words to allow matches to be found despite the presence of a mismatch. It also provides a search mode using a query STS against a sequence database.
NetPrimer
Combines the latest primer analysis algorithms with a web-based interface allowing the user to analyze primers over the Internet.
dnaMATE
This server calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) using a merged method that is based on three different thermodynamic tables.
MELTING
Computes the enthalpy, the entropy and the melting temperature of the helix-coil transitions for a nucleic acid duplex. MELTING uses approximate formulae or Nearest-Neighbor approaches. The software provides a large set of thermodynamic models and can manage four type of hybridization. Some formulas are available to correct temperature for monovalent ions (sodium, potassium, Tris), magnesium ions, formamide and dimethyl sulfoxide (DMSO).
OligoCalc / Oligonucleotide properties Calculator
A web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties.
OligoAnalyzer
Allows prediction of several kinds of information about an oligonucleotide sequence. OligoAnalyzer is a central calculator enabling comprehensive oligonucleotide analysis. Selection of the analyze button results in the physical properties of the oligonucleotide, such as a complementary sequence, oligonucleotide length, content of G and C bases, melting temperature, extinction coefficient at 260 nm and molecular weight. The software was designed to position locked nucleic acids (LNA) modifications within a sequence, so that the desired melting temperature of the duplex sequence is achieved.
OligoEvaluator
An online oligonucleotide sequence calculator. OligoEvaluator is easy to use: register or login, select DNA or RNA, paste your sequence and click calculate. All reported properties are available for export to a convenient Excel template.
PerlPrimer
A free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing.
MFEprimer
Allows users to check primer specificity against genomic DNA and messenger RNA/complementary DNA sequence databases. MFEprimer is a tool that processes in four steps: (1) finds all of the binding-site positions of the 30 -end subsequence of a primer among all possible DNA template sequences; (2) evaluates the binding stability of the entire primer sequence using the nearest-neighbour (NN) model; (3) runs a virtual polymerase chain reaction (PCR) amplification; and (4) filters out the predicted amplicons by size and other parameters.
Primaclade
Designs minimally degenerate primers for comparative studies of multiple species. Primaclade is a web-based primer prediction application that provides a solution for researchers who want to design Polymerase Chain Reaction (PCR) primers across multiple species. The software generally performed best with alignments of up to about eight sequences and up to 29.0% sequence divergence. It can simplify the design of PCR primers for any comparative molecular study.