Bisulfite primer design software tools | Bisulfite sequencing data analysis
The major obstacle of bisulfite sequencing PCR is the reduced complexity of DNA sequences in gene promoter regions and especially CpG islands. These genomic loci have elevated GC content and lowered complexity, compared with protein-coding regions. Bisulfite treatment aggravates the situation resulting in the reduction of the four-letter alphabet to the three-letter one, except for methylated cytosines which are not converted to thymines. This strikingly decreases sequence complexity, increases mispriming and dimer-forming potential, reduces GC content, and leads to the formation of large polyT motifs. As a result, primer design is very problematic and nested PCR sometimes is required to avoid non-specific amplification.
Improves the design and use of polymerase chain reaction (PCR)-based methylation assays. methPrimer was developed to store and retrieve validated methylation assays. This resource is intended to be a search portal for validated methylation assays. It also aims to establish a certain level of standardization and uniformity in the use of PCR based methylation assays. Each primer set is provided with a unique identifier to access them directly or refer to in a publication.
Serves for designing quantitative DNA methylation experiments for Agena Bioscience's EpiTYPER technology. EpiDesigner is a web application allowing users to design primers for bisulfite treated genomic DNA and recommend primer pairs for individual assays.
A web-based tool for bisulfite sequencing analysis. Kismeth was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species. Kismeth simplifies bisulfite sequencing analysis. It is the only publicly available tool for the design of bisulfite primers for plants, and one of the few tools for the analysis of methylation patterns in plants.
Provides a web server to design for the amplification of single templates. BiSearch is a useful tool in primer design for complex matrices and especially for bisulfite-treated genomes. It can be utilized for any DNA template; however, it is especially suited for primer design for chemically modified DNA used to determine the CpG methylation profile of a DNA template by the bisulfite genomic sequencing technique.
Allows users to support bisulfite polymerase chain reaction (PCR) and multiplex PCR assay. PrimerSuite is a web application that generates all possible primers by walking along the region of interest one base at a time. It can compute the melting temperature of the oligonucleotides based on the salt-adjusted melting temperature with each primer pair filtered according to the parameters as specified by users.
Serves for high-throughput primer and probe design. PRIMEGENS contains functionalities assisting users to select genomic regions and to design primer/probe for selected regions in an automatic fashion. This program is available as a standalone named PRIMEGENSv2 and a web application named PRIMEGENSw3. The web application allows users to: upload their own genomic sequences, design primers, filter them based on cross-hybridization, and then view the resulting primers.