Customized RNA synthesis is in demand for biological and biotechnological research. While chemical synthesis and gel or chromatographic purification of RNA is costly and difficult for sequences longer than tens of nucleotides, a pipeline of primer assembly of DNA templates, in vitro transcription by T7 RNA polymerase and kit-based purification provides a cost-effective and fast alternative for preparing RNA molecules. Nevertheless, designing template primers that optimize cost and avoid mispriming during polymerase chain reaction currently requires expert inspection, downloading specialized software or both.
Scans automatically target DNA sequences and designs primers in regions of low degeneracy that are free of secondary structures (hairpins, dimers and false priming sites). Primer Premier searches for optimal polymerase chain reaction (PCR), multiplex and single nucleotide polymorphism (SNP) genotyping primers via a nearest neighbor algorithm. It supports multiplex assays and can automatically describe BLAST search results.
Addresses the challenges of bacterial identification, pathogen detection or species identification. AlleleID is a comprehensive desktop tool to design species identification/cross species probes for microarrays or real time polymerase chain reaction (PCR) including SYBR Green, TaqMan MGB, TaqMan probes, Molecular Beacons and real time PCR primers. AlleleID also offers support for designing microarray experiments for detecting alternative splicing events.
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 scientists to design, share, and record experiments or tests. The Benchling platform contains a Biological Registration System, an Electronic Lab Notebook, and Molecular Biology Design and Analysis Suite. This platform is made for scientists from pharma and biotech companies like government or academic labs. It permits users to share projects with co-worker and to control access to these projects.
Predicts microsatellite molecular marker development. WebSat permits to submit sequences, and visualize microsatellites. It allows user to amplify and export the resulting data thank to design of primers suitable. The tool does not support large data sets. It returns the sequence identification, Simple sequence repeats (SSR), the product size, forward and reverse primer sequence, melting temperature, and coordinates of the primers within the sequence.
Automates the design of mutagenic polymerase chain reaction (PCR) primers for site-directed mutagenesis. PrimerX works in 4 steps: It (i) compares a template DNA sequence with a DNA or protein sequence, (ii) generates forward primer sequences by computing for all possible oligonucleotide sequences of appropriate length, (iii) generates corresponding reverse primer sequences, and (iv) computes for other necessary information such as melting temperature and GC content for each primer pair.
Calculates covariance scores for constrained regions of background conservation. McBASC can be utilized as a covarying or highly conserved filter. This software gives an equally high score to conserved or covarying alignments and allows, without a reduction in score, substitution of conserved pairs of residues for covarying ones.