In silico PCR software tools | Quantitative PCR data analysis
The development of the DNA sequencing technology and in particularly the emergence of high-throughput sequencing (HTS) has led to progressive accumulation of huge amounts of raw genome sequence data. For this reason, there is a growing demand for in silico approaches to extract useful information from raw sequence data, process the information using virtual tools and predict experimental results already at the planning stage. One such approach is in silico PCR. The usual goal of in silico PCR is to predict which PCR products are synthesized from one or multiple DNA templates. Other common goals include template sequence location in the genome as well as primer/probe design and analysis, such as prediction of melting temperatures and secondary/tetriary structures including hairpins, G-quadruplexes, self-dimers and cross-dimers in primer pairs.
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.
Allows users to estimate Barcode primers quality. ecoPCR is an electronic Polymerase Chain Reaction (PCR) software which helps to compute barcode coverage and barcode specificity. It preserves the information about taxonomic and supplies various specified conditions for the in silico amplification.
Aims to simplify the manipulation of sequence files. OBITools is a set of python programs specifically designed for analysing NGS data. It allows users to set up versatile data analysis pipelines, adjustable to the broad range of DNA metabarcoding applications. As inputs, this package is able to automatically recognize the most common sequence file formats.
Simulates Polymerase chain reaction (PCR) given a list of sequences in FASTA or Genbank format. WebPCR is a web app that simulates PCR given primers and a template sequence. The last sequence in the list is interpreted as template and the preceding ones as primers. For each potential PCR product, a report will be generated containing the PCR product sequence and some additional data. It is a python program running in the cloud on a free Google app engine.
Introduces concepts of multi-factorial experimental design and supports teaching of the polymerase chain reaction. PCR Simulator is an on-line application modelled on laboratory protocols for performing the PCR. The software provides a virtual experience of a complex laboratory protocol with the simulated reactions qualitatively matching real experiments. It enables users to generate data for their own analysis within the teaching environment, allowing combined teaching of experimental design and experimental analysis.