Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
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.
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.
Aims to calculate oligonucleotide dilutions. Dilution Calculator returns volumes used to mix solutions. It takes as input an initial concentration, a volume and the desired final concentration. This tool can be brought directly from the Oligo Analyzer results. It is available on a web platform that provides a user-friendly interface.
Estimates the volume of solution needed to achieve a specific concentration when known moles or mass of dry oligonucleotide are dissolved. Resuspension Calculator can be brought directly from the Oligo Analyzer results. It needs as input a quantity of oligonucleotide and the final desired concentration. This tool is accessible through a web user interface.
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.
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).
Provides a freely accessible, central platform for rapid specificity and coverage evaluations of probes and primers against the latest sequence collections of selected phylogenetic and functional marker genes. Using a common user interface a number of established sequence databases can be queried.
Combines automated small subunit (SSU) primer evaluation with rRNA gene extraction and classification for the analysis of shotgun metagenomic and metatranscriptomic datasets. MIPE is a metagenome based community structure explorer and primer evaluation tool. With a metagenome dataset input, it demonstrates the detailed composition taxonomy information, and the coverage of the primer of interest.
Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt.
Enables in silico evaluation of primers and probes intended for routinely employed quantitative reverse transcriptase real-time polymerase chain reaction (RT-qPCR). SCREENED extracts the targeted genomic regions in the analyzed genomes and then assesses whether primers and probes will successfully anneal resulting in signal detection. The software was used to compare routinely employed RT-qPCR methods for dengue virus detection. It can serve for evaluating RT-qPCR method performance for other viral species.
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.